FAIRsharing.wjzty; Last edited: April 26, 2021, 11:38 a.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.541292

SCOP2 - Structural Classification Of Proteins
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

scop
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.541292

Other names: SCOP, SCOP2 - Structural Classification Of Proteins, scop

The SCOP database is a curated both manually and with the use of automated tools. This freely available resource aims to provide a comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known.

Webpage:

http://scop.mrc-lmb.cam.ac.uk/scop

Licence:

Name: SCOP Attribution required
URL: http://scop.mrc-lmb.cam.ac.uk/

Publications: (9)

Publications
More detailed information about this field from each metasource.

SCOP: a structural classification of proteins database for the investigation of sequences and structures
PMID: 7723011
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.541292

Data growth and its impact on the SCOP database: new developments
PMID: 18000004
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.541292

SCOP database in 2004: refinements integrate structure and sequence family data
PMID: 14681400
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.541292

SCOP: a structural classification of proteins database
PMID: 10592240
metasource: Fairsharing.org
version: FAIRsharing.org: SCOP; Structural Classification Of Proteins; DOI: https://doi.org/10.25504/FAIRsharing.wjzty; Last edited: April 26, 2021, 11:38 a.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.541292

SCOP database in 2002: refinements accommodate structural genomics
PMID: 11752311
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.541292

SCOP: a structural classification of proteins database
PMID: 9016544
metasource: Fairsharing.org
version: FAIRsharing.org: SCOP; Structural Classification Of Proteins; DOI: https://doi.org/10.25504/FAIRsharing.wjzty; Last edited: April 26, 2021, 11:38 a.m.; Last accessed: Jan 03 2022 7:08 p.m.

SCOP: a Structural Classification of Proteins database
PMID: 9847194
metasource: Fairsharing.org
version: FAIRsharing.org: SCOP; Structural Classification Of Proteins; DOI: https://doi.org/10.25504/FAIRsharing.wjzty; Last edited: April 26, 2021, 11:38 a.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:09.541292

SCOP, Structural Classification of Proteins database: applications to evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data
PMID: 10089491
metasource: Fairsharing.org
version: FAIRsharing.org: SCOP; Structural Classification Of Proteins; DOI: https://doi.org/10.25504/FAIRsharing.wjzty; Last edited: April 26, 2021, 11:38 a.m.; Last accessed: Jan 03 2022 7:08 p.m.

http://dx.doi.org/10.1093/nar/gkt1242
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

SCOP: a structural classification of proteins database for the investigation of sequences and structures PubMed citations: 2016.

2016 articles citing: SCOP: a structural classification of proteins database for the investigation of sequences and structures

Survey of the Intermolecular Disulfide Bonds Observed in Protein Crystal Structures Deposited in the Protein Data Bank. PMID:35888076
A consensus view of the proteome of the last universal common ancestor. PMID:35784055
Bridging the gaps in statistical models of protein alignment. PMID:35758809
On the reliability and the limits of inference of amino acid sequence alignments. PMID:35758808
Evaluating hierarchical machine learning approaches to classify biological databases. PMID:35724625
The Structural Rule Distinguishing a Superfold: A Case Study of Ferredoxin Fold and the Reverse Ferredoxin Fold. PMID:35684484
What Is Parvalbumin for? PMID:35625584
Three-dimensional Structure Databases of Biological Macromolecules. PMID:35507259
Protection of lead-induced cytotoxicity using paramagnetic nickel-insulin quantum clusters. PMID:35481039
Hierarchical representation for PPI sites prediction. PMID:35307006
PyUUL provides an interface between biological structures and deep learning algorithms. PMID:35181656
The aqueous humor proteome is intrinsically disordered. PMID:35128080
Erythropoietin Interacts with Specific S100 Proteins. PMID:35053268
The impact of AlphaFold2 one year on. PMID:35017725
AMPing Up the Search: A Structural and Functional Repository of Antimicrobial Peptides for Biofilm Studies, and a Case Study of Its Application to Corynebacterium striatum, an Emerging Pathogen. PMID:34976872
SCOPe: improvements to the structural classification of proteins - extended database to facilitate variant interpretation and machine learning. PMID:34850923
Discovering the Ultimate Limits of Protein Secondary Structure Prediction. PMID:34827624
Functional Annotation from Structural Homology. PMID:34718998
Implications of divergence of methionine adenosyltransferase in archaea. PMID:34655277
FoldHSphere: deep hyperspherical embeddings for protein fold recognition. PMID:34641786
The ubiquitous buried water in the beta-trefoil architecture contributes to the folding nucleus and ~20% of the folding enthalpy. PMID:34562298
Comparative Two-dimensional Gel Electrophoresis Maps for Amastigote-like Proteomes of Iranian Leishmania Tropica and Leishmania Major Isolates. PMID:34466522
Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design. PMID:34423306
Capabilities of bioinformatics tools for optimizing physicochemical features of proteins used in Nano biosensors: A short overview of the tools related to bioinformatics. PMID:34401530
Potential stress tolerance roles of barley germins and GLPs. PMID:34363524
Comparative Evaluation of Shape Retrieval Methods on Macromolecular Surfaces: An Application of Computer Vision Methods in Structural Bioinformatics. PMID:34247232
The urgent need for metallo-β-lactamase inhibitors: an unattended global threat. PMID:34246322
The variation among sites of protein structure divergence is shaped by mutation and scaled by selection. PMID:34235475
Computational-Driven Epitope Verification and Affinity Maturation of TLR4-Targeting Antibodies. PMID:34206009
Critical assessment of coiled-coil predictions based on protein structure data. PMID:34127723
Evolution of networks of protein domain organization. PMID:34103558
Using Recursive Feature Selection with Random Forest to Improve Protein Structural Class Prediction for Low-Similarity Sequences. PMID:34055035
Protein Structure Prediction: Conventional and Deep Learning Perspectives. PMID:34050498
Tracing Evolution Through Protein Structures: Nature Captured in a Few Thousand Folds. PMID:34041266
Abundance Imparts Evolutionary Constraints of Similar Magnitude on the Buried, Surface, and Disordered Regions of Proteins. PMID:33996892
Universal Architectural Concepts Underlying Protein Folding Patterns. PMID:33996891
Fast computational mutation-response scanning of proteins. PMID:33976988
The order of PDZ3 and TrpCage in fusion chimeras determines their properties-a biophysical characterization. PMID:33969912
Master Blaster: an approach to sensitive identification of remotely related proteins. PMID:33888741
Recombinant Production and Characterization of an Extracellular Subtilisin-Like Serine Protease from Acinetobacter baumannii of Fermented Food Origin. PMID:33870461
Enhancement of conformational B-cell epitope prediction using CluSMOTE. PMID:33816926
Hinge-shift mechanism as a protein design principle for the evolution of β-lactamases from substrate promiscuity to specificity. PMID:33767175
Genome-wide identification of F-box proteins in Macrophomina phaseolina and comparison with other fungus. PMID:33761027
Estimating transition path times and shapes from single-molecule photon trajectories: A simulation analysis. PMID:33752373
Protein Interaction Interface Region Prediction by Geometric Deep Learning. PMID:33693581
SSnet: A Deep Learning Approach for Protein-Ligand Interaction Prediction. PMID:33573266
Cofactors are Remnants of Life's Origin and Early Evolution. PMID:33547911
Development of a TSR-Based Method for Protein 3-D Structural Comparison With Its Applications to Protein Classification and Motif Discovery. PMID:33520934
Bridging Themes: Short Protein Segments Found in Different Architectures. PMID:33502503
Structural and Biochemical Analysis Reveals a Distinct Catalytic Site of Salicylate 5-Monooxygenase NagGH from Rieske Dioxygenases. PMID:33452034
Overexpression of the Bacteriophage T4 motB Gene Alters H-NS Dependent Repression of Specific Host DNA. PMID:33435393
A Fifth of the Protein World: Rossmann-like Proteins as an Evolutionarily Successful Structural unit. PMID:33387532
MoonProt 3.0: an update of the moonlighting proteins database. PMID:33245761
A complete rule set for designing symmetry combination materials from protein molecules. PMID:33239442
DeepFrag-k: a fragment-based deep learning approach for protein fold recognition. PMID:33203392
Mutations in the SARS-CoV-2 spike RBD are responsible for stronger ACE2 binding and poor anti-SARS-CoV mAbs cross-neutralization. PMID:33200028
Conserved patterns and interactions in the unfolding transition state across SH3 domain structural homologues. PMID:33190305
Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase. PMID:33079059
Crystal structure of tomato spotted wilt virus GN reveals a dimer complex formation and evolutionary link to animal-infecting viruses. PMID:33020295
Plant Antimicrobial Peptides: State of the Art, In Silico Prediction and Perspectives in the Omics Era. PMID:32952397
Sequence alignment generation using intermediate sequence search for homology modeling. PMID:32802276
A New Protocol for Atomic-Level Protein Structure Modeling and Refinement Using Low-to-Medium Resolution Cryo-EM Density Maps. PMID:32771523
Network-based protein structural classification. PMID:32742675
Real time structural search of the Protein Data Bank. PMID:32639954
Network analysis of synonymous codon usage. PMID:32609328
A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community). PMID:32566135
β-Strand-mediated interactions of protein domains. PMID:32543729
Structure and Electron-Transfer Pathway of the Human Methionine Sulfoxide Reductase MsrB3. PMID:32517586
Multidomain protein structure prediction using information about residues interacting on multimeric protein interfaces. PMID:32509489
An Evidence-Based Update on the Molecular Mechanisms Underlying Periodontal Diseases. PMID:32481582
The large family of PC4-like domains - similar folds and functions throughout all kingdoms of life. PMID:32476604
Intrinsic Disorder in Tetratricopeptide Repeat Proteins. PMID:32466138
A 2-Tyr-1-carboxylate Mononuclear Iron Center Forms the Active Site of a Paracoccus Dimethylformamidase. PMID:32452120
Structure of the SARS-Unique Domain C From the Bat Coronavirus HKU4. PMID:32395093
Structural and functional properties of proteins interacting with small heat shock proteins. PMID:32314314
Investigation of sequence features of hinge-bending regions in proteins with domain movements using kernel logistic regression. PMID:32272894
The macrodomain family: Rethinking an ancient domain from evolutionary perspectives. PMID:32214744
Pseudo-Symmetric Assembly of Protodomains as a Common Denominator in the Evolution of Polytopic Helical Membrane Proteins. PMID:32189026
NBCZone: Universal three-dimensional construction of eleven amino acids near the catalytic nucleophile and base in the superfamily of (chymo)trypsin-like serine fold proteases. PMID:32151723
ALEPH: a network-oriented approach for the generation of fragment-based libraries and for structure interpretation. PMID:32133985
Ab Initio Construction and Evolutionary Analysis of Protein-Coding Gene Families with Partially Homologous Relationships: Closely Related Drosophila Genomes as a Case Study. PMID:32108239
The acid-base-nucleophile catalytic triad in ABH-fold enzymes is coordinated by a set of structural elements. PMID:32084230
On the evolution of protein-adenine binding. PMID:32079721
FTIP: an accurate and efficient method for global protein surface comparison. PMID:32022843
How to choose templates for modeling of protein complexes: Insights from benchmarking template-based docking. PMID:31994759
The basis for non-canonical ROK family function in the N-acetylmannosamine kinase from the pathogen Staphylococcus aureus. PMID:31949045
Mapping Multiple Distances in a Multidomain Protein for the Identification of Folding Intermediates. PMID:31916943
UDSMProt: universal deep sequence models for protein classification. PMID:31913448
Factors influencing estimates of coordinate error for molecular replacement. PMID:31909740
MADOKA: an ultra-fast approach for large-scale protein structure similarity searching. PMID:31870277
Functional analysis of Rossmann-like domains reveals convergent evolution of topology and reaction pathways. PMID:31869345
Shared unfolding pathways of unrelated immunoglobulin-like β-sandwich proteins. PMID:31868211
Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation. PMID:31733063
The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures. PMID:31724711
DALI and the persistence of protein shape. PMID:31606894
Reporting on the future of integrative structural biology ORAU workshop. PMID:31585877
Structural characterization of a prolyl aminodipeptidase (PepX) from Lactobacillus helveticus. PMID:31584010
Molecular function limits divergent protein evolution on planetary timescales. PMID:31532392
Predicting Sequence Features, Function, and Structure of Proteins Using MESSA. PMID:31524991
Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis. PMID:31523127
Statistical compression of protein sequences and inference of marginal probability landscapes over competing alignments using finite state models and Dirichlet priors. PMID:31510703
Comprehensive classification of the plant non-specific lipid transfer protein superfamily towards its sequence-structure-function analysis. PMID:31428542
Integrating ab initio and template-based algorithms for protein-protein complex structure prediction. PMID:31393558
Unraveling the structural landscape of intra-chain domain interfaces: Implication in the evolution of domain-domain interactions. PMID:31374091
Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids. PMID:31366885
Protein tertiary structure and the myoglobin phase diagram. PMID:31346242
FunFam protein families improve residue level molecular function prediction. PMID:31319797
C7orf59/LAMTOR4 phosphorylation and structural flexibility modulate Ragulator assembly. PMID:31314152
Interfaces Between Alpha-helical Integral Membrane Proteins: Characterization, Prediction, and Docking. PMID:31303974
Intrinsically disordered domains: Sequence ➔ disorder ➔ function relationships. PMID:31299122
Fold combinations in multi-domain proteins. PMID:31249437
Semi-rational evolution of the 3-(3-hydroxyalkanoyloxy)alkanoate (HAA) synthase RhlA to improve rhamnolipid production in Pseudomonas aeruginosa and Burkholderia glumae. PMID:31177633
Genome analysis provides insight about pathogenesis of Indian strains of Rhizoctonia solani in rice. PMID:31102065
Geometric description of self-interaction potential in symmetric protein complexes. PMID:31101822
Oxidative opening of the aromatic ring: Tracing the natural history of a large superfamily of dioxygenase domains and their relatives. PMID:31092555
Computational Characterization of the mtORF of Pocilloporid Corals: Insights into Protein Structure and Function in Stylophora Lineages from Contrasting Environments. PMID:31035578
Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm. PMID:31009453
Translation-coupled protein folding assay using a protease to monitor the folding status. PMID:30993770
Study of correlations between protein peptide plane dynamics and side chain dynamics. PMID:30978222
A global map of the protein shape universe. PMID:30978181
A comprehensive in silico analysis of sortase superfamily. PMID:30900148
Testing Empirical Support for Evolutionary Models that Root the Tree of Life. PMID:30887086
Classification of the human THAP protein family identifies an evolutionarily conserved coiled coil region. PMID:30836974
PASS2 version 6: a database of structure-based sequence alignments of protein domain superfamilies in accordance with SCOPe. PMID:30820573
Density fields for branching, stiff networks in rigid confining regions. PMID:30788631
Selecting Near-Native Protein Structures from Predicted Decoy Sets Using Ordered Graphlet Degree Similarity. PMID:30754721
Functional Evolution of Proteins. PMID:30714210
Genome-Wide Analysis of Domain-Swap Predicted Products in the Genome of Anti-Stress Medicinal Plant: Ocimum tenuiflorum. PMID:30692846
Proteome-wide, Structure-Based Prediction of Protein-Protein Interactions/New Molecular Interactions Viewer. PMID:30679268
RRMdb-an evolutionary-oriented database of RNA recognition motif sequences. PMID:30649297
An improved protein structure evaluation using a semi-empirically derived structure property. PMID:30541545
Protein-protein interaction sites prediction by ensemble random forests with synthetic minority oversampling technique. PMID:30520961
SCOPe: classification of large macromolecular structures in the structural classification of proteins-extended database. PMID:30500919
The Site-Specific Amino Acid Preferences of Homologous Proteins Depend on Sequence Divergence. PMID:30496400
Automated shape-based clustering of 3D immunoglobulin protein structures in chronic lymphocytic leukemia. PMID:30453883
Computational discovery of direct associations between GO terms and protein domains. PMID:30453875
The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver. PMID:30445555
Design of metalloproteins and novel protein folds using variational autoencoders. PMID:30385875
Cross-strand disulfides in the hydrogen bonding site of antiparallel β-sheet (aCSDhs): Forbidden disulfides that are highly strained, easily broken. PMID:30383331
What is an archaeon and are the Archaea really unique? PMID:30357005
Gene Gangs of the Chloroviruses: Conserved Clusters of Collinear Monocistronic Genes. PMID:30347809
Retraction: Site‐specific recombination of nitrogen‐fixation genes in cyanobacteria by XisF–XisH–XisI complex: Structures and models, William C. Hwang, James W. Golden, Jaime Pascual, Dong Xu, Anton Cheltsov, Adam Godzik. PMID:30338965
Multi-criteria protein structure comparison and structural similarities analysis using pyMCPSC. PMID:30332415
Distinctive structural motifs co-ordinate the catalytic nucleophile and the residues of the oxyanion hole in the alpha/beta-hydrolase fold enzymes. PMID:30311984
The bacterial Ras/Rap1 site-specific endopeptidase RRSP cleaves Ras through an atypical mechanism to disrupt Ras-ERK signaling. PMID:30279169
Effects of protein size, thermodynamic stability, and net charge on cotranslational folding on the ribosome. PMID:30224455
DaReUS-Loop: accurate loop modeling using fragments from remote or unrelated proteins. PMID:30209260
Insights on a putative aminoacyl-tRNA-protein transferase of Leishmania major. PMID:30208112
Binding site matching in rational drug design: algorithms and applications. PMID:30169563
Grxcr2 is required for stereocilia morphogenesis in the cochlea. PMID:30157177
PPInS: a repository of protein-protein interaction sitesbase. PMID:30127348
P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure. PMID:30109435
Searching ECOD for Homologous Domains by Sequence and Structure. PMID:30040199
Highly active enzymes by automated combinatorial backbone assembly and sequence design. PMID:30018322
Study of specific nanoenvironments containing α-helices in all-α and (α+β)+(α/β) proteins. PMID:29990352
SIMBAD: a sequence-independent molecular-replacement pipeline. PMID:29968670
SDADB: a functional annotation database of protein structural domains. PMID:29961821
A novel methodology on distributed representations of proteins using their interacting ligands. PMID:29949957
Sequence-based prediction of physicochemical interactions at protein functional sites using a function-and-interaction-annotated domain profile database. PMID:29859055
Mining of potential drug targets through the identification of essential and analogous enzymes in the genomes of pathogens of Glycine max, Zea mays and Solanum lycopersicum. PMID:29799863
Automated method to differentiate between native and mirror protein models obtained from contact maps. PMID:29787567
RBLOSUM performs better than CorBLOSUM with lesser error per query. PMID:29784028
Nonnative Energetic Frustrations in Protein Folding at Residual Level: A Simulation Study of Homologous Immunoglobulin-like β-Sandwich Proteins. PMID:29783701
High-throughput discovery of functional disordered regions: investigation of transactivation domains. PMID:29759983
The tale of two talins - two isoforms to fine-tune integrin signalling. PMID:29723415
ENTPRISE-X: Predicting disease-associated frameshift and nonsense mutations. PMID:29723276
Interaction of the GntR-family transcription factor Sll1961 with thioredoxin in the cyanobacterium Synechocystis sp. PCC 6803. PMID:29703909
Evolutionary convergence and divergence in archaeal chromosomal proteins and Chromo-like domains from bacteria and eukaryotes. PMID:29670199
Stabilization of warfarin-binding pocket of VKORC1 and VKORL1 by a peripheral region determines their different sensitivity to warfarin inhibition. PMID:29665197
An antibody with Fab-constant domains exchanged for a pair of CH3 domains. PMID:29630643
Functional classification of protein structures by local structure matching in graph representation. PMID:29604149
Effects of pH and aggregation in the human prion conversion into scrapie form: a study using molecular dynamics with excited normal modes. PMID:29546436
Recent developments in MrBUMP: better search-model preparation, graphical interaction with search models, and solution improvement and assessment. PMID:29533225
Comparative assessment of strategies to identify similar ligand-binding pockets in proteins. PMID:29523085
Mutations in CFAP43 and CFAP44 cause male infertility and flagellum defects in Trypanosoma and human. PMID:29449551
Choosing non-redundant representative subsets of protein sequence data sets using submodular optimization. PMID:29345009
Visualization and analysis of non-covalent contacts using the Protein Contacts Atlas. PMID:29335563
Large-scale aggregation analysis of eukaryotic proteins reveals an involvement of intrinsically disordered regions in protein folding. PMID:29330519
DeepSF: deep convolutional neural network for mapping protein sequences to folds. PMID:29228193
Using bioinformatic and phylogenetic approaches to classify transposable elements and understand their complex evolutionary histories. PMID:29225705
Novel Families of Archaeo-Eukaryotic Primases Associated with Mobile Genetic Elements of Bacteria and Archaea. PMID:29198957
Rapid and reliable protein structure determination via chemical shift threading. PMID:29196969
Template-based quaternary structure prediction of proteins using enhanced profile-profile alignments. PMID:29178285
Oxygen Activation by Cu LPMOs in Recalcitrant Carbohydrate Polysaccharide Conversion to Monomer Sugars. PMID:29155571
Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction. PMID:29136098
Random protein sequences can form defined secondary structures and are well-tolerated in vivo. PMID:29133927
PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. PMID:29126160
GRAFENE: Graphlet-based alignment-free network approach integrates 3D structural and sequence (residue order) data to improve protein structural comparison. PMID:29097661
The crystal structure of the Yersinia pestis iron chaperone YiuA reveals a basic triad binding motif for the chelated metal. PMID:29095164
Interdependence, Reflexivity, Fidelity, Impedance Matching, and the Evolution of Genetic Coding. PMID:29077934
Evidence of evolutionary selection for cotranslational folding. PMID:29073068
RNArchitecture: a database and a classification system of RNA families, with a focus on structural information. PMID:29069520
Intramembrane Thiol Oxidoreductases: Evolutionary Convergence and Structural Controversy. PMID:29064673
Forecasting residue-residue contact prediction accuracy. PMID:29036497
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. PMID:29035372
Protein remote homology detection based on bidirectional long short-term memory. PMID:29017445
The folded k-spectrum kernel: A machine learning approach to detecting transcription factor binding sites with gapped nucleotide dependencies. PMID:28982128
SupeRNAlign: a new tool for flexible superposition of homologous RNA structures and inference of accurate structure-based sequence alignments. PMID:28934487
PDBsum: Structural summaries of PDB entries. PMID:28875543
Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group. PMID:28872143
Structural and Functional View of Polypharmacology. PMID:28860623
Rules for connectivity of secondary structure elements in protein: Two-layer αβ sandwiches. PMID:28856751
Functional Analogy in Human Metabolism: Enzymes with Different Biological Roles or Functional Redundancy? PMID:28854631
Elastic network model of learned maintained contacts to predict protein motion. PMID:28854238
The Enigmatic Origin of Papillomavirus Protein Domains. PMID:28832519
Evolutionary analysis of a novel zinc ribbon in the N-terminal region of threonine synthase. PMID:28820334
Uncoupling conformational states from activity in an allosteric enzyme. PMID:28781362
B3GAT3-related disorder with craniosynostosis and bone fragility due to a unique mutation. PMID:28771243
Predictions of Backbone Dynamics in Intrinsically Disordered Proteins Using De Novo Fragment-Based Protein Structure Predictions. PMID:28765603
Structure of Chorismate Mutase-like Domain of DAHPS from Bacillus subtilis Complexed with Novel Inhibitor Reveals Conformational Plasticity of Active Site. PMID:28743924
Structural insights into transcription initiation by yeast RNA polymerase I. PMID:28739580
Community detection in sequence similarity networks based on attribute clustering. PMID:28738060
UCSF ChimeraX: Meeting modern challenges in visualization and analysis. PMID:28710774
DprA from Neisseria meningitidis: properties and role in natural competence for transformation. PMID:28696187
1.8 Å resolution crystal structure of the carbapenem intrinsic resistance protein CarF. PMID:28695855
Computational and Experimental Studies of ADP-Ribosylation. PMID:28695527
Molecular cloning and biochemical characterization of two cation chloride cotransporter subfamily members of Hydra vulgaris. PMID:28662098
Resurrecting the Dead (Molecules). PMID:28652896
3D deep convolutional neural networks for amino acid environment similarity analysis. PMID:28615003
A tensegrity model for hydrogen bond networks in proteins. PMID:28607953
Evolution of intrinsic disorder in eukaryotic proteins. PMID:28597295
PFASUM: a substitution matrix from Pfam structural alignments. PMID:28583067
Insights into PG-binding, conformational change, and dimerization of the OmpA C-terminal domains from Salmonella enterica serovar Typhimurium and Borrelia burgdorferi. PMID:28580643
Comprehensive classification of the PIN domain-like superfamily. PMID:28575517
Databases, Repositories, and Other Data Resources in Structural Biology. PMID:28573593
Severe child form of primary hyperoxaluria type 2 - a case report revealing consequence of GRHPR deficiency on metabolism. PMID:28569194
XSuLT: a web server for structural annotation and representation of sequence-structure alignments. PMID:28510698
Allosteric movements in eubacterial RecA. PMID:28510107
ThreaDomEx: a unified platform for predicting continuous and discontinuous protein domains by multiple-threading and segment assembly. PMID:28498994
Widespread position-specific conservation of synonymous rare codons within coding sequences. PMID:28475588
The natural history of molecular functions inferred from an extensive phylogenomic analysis of gene ontology data. PMID:28467492
Oncodomains: A protein domain-centric framework for analyzing rare variants in tumor samples. PMID:28426665
Characterization of protein folding by a Φ-value calculation with a statistical-mechanical model. PMID:28409079
The H3 loop of antibodies shows unique structural characteristics. PMID:28342222
Structural insights into the γ-lactamase activity and substrate enantioselectivity of an isochorismatase-like hydrolase from Microbacterium hydrocarbonoxydans. PMID:28295028
Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions. PMID:28280526
Improving prediction of helix-helix packing in membrane proteins using predicted contact numbers as restraints. PMID:28263405
A New Reference Genome Assembly for the Microcrustacean Daphnia pulex. PMID:28235826
A three-way approach for protein function classification. PMID:28234929
ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains. PMID:28193156
An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins. PMID:28187133
Identifying the missing proteins in human proteome by biological language model. PMID:28155671
Aberrant coordination geometries discovered in the most abundant metalloproteins. PMID:28142195
Drosophila CG3303 is an essential endoribonuclease linked to TDP-43-mediated neurodegeneration. PMID:28139767
TIR-only protein RBA1 recognizes a pathogen effector to regulate cell death in Arabidopsis. PMID:28137883
An ambiguity principle for assigning protein structural domains. PMID:28097215
Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. PMID:28092920
Protein sequence-similarity search acceleration using a heuristic algorithm with a sensitive matrix. PMID:28083762
Prediction of Local Quality of Protein Structure Models Considering Spatial Neighbors in Graphical Models. PMID:28074879
Sixty-five years of the long march in protein secondary structure prediction: the final stretch? PMID:28040746
Recent Progress in Machine Learning-Based Methods for Protein Fold Recognition. PMID:27999256
Mapping the membrane proteome of anaerobic gut fungi identifies a wealth of carbohydrate binding proteins and transporters. PMID:27998268
The evolution of function within the Nudix homology clan. PMID:27936487
Piecemeal Buildup of the Genetic Code, Ribosomes, and Genomes from Primordial tRNA Building Blocks. PMID:27918435
A closer look into the α-helix basin. PMID:27917894
SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins - extended Database. PMID:27914894
Enhanced fold recognition using efficient short fragment clustering. PMID:27882309
Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23. PMID:27881076
Rice Cellulose SynthaseA8 Plant-Conserved Region Is a Coiled-Coil at the Catalytic Core Entrance. PMID:27879387
Establishing a reference array for the CS-αβ superfamily of defensive peptides. PMID:27863510
Similarity search for local protein structures at atomic resolution by exploiting a database management system. PMID:27857569
Possible roles of S···O and S···N interactions in the functions and evolution of phospholipase A2. PMID:27857557
Predicting secondary structures, contact numbers, and residue-wise contact orders of native protein structures from amino acid sequences using critical random networks. PMID:27857554
Melody discrimination and protein fold classification. PMID:27812548
Multi-omic data integration enables discovery of hidden biological regularities. PMID:27782110
Structural Interface Forms and Their Involvement in Stabilization of Multidomain Proteins or Protein Complexes. PMID:27763556
Bioinformatics and functional analyses of coronavirus nonstructural proteins involved in the formation of replicative organelles. PMID:27743916
An efficient algorithm for protein structure comparison using elastic shape analysis. PMID:27708689
Development of a motif-based topology-independent structure comparison method to identify evolutionarily related folds. PMID:27671894
ProFold: Protein Fold Classification with Additional Structural Features and a Novel Ensemble Classifier. PMID:27660761
Genome-wide survey and phylogeny of S-Ribosylhomocysteinase (LuxS) enzyme in bacterial genomes. PMID:27650568
Topology independent comparison of RNA 3D structures using the CLICK algorithm. PMID:27634929
A new definition and properties of the similarity value between two protein structures. PMID:27623799
Origin of a folded repeat protein from an intrinsically disordered ancestor. PMID:27623012
Protein secondary structure prediction using a small training set (compact model) combined with a Complex-valued neural network approach. PMID:27618812
Substrate specificity characterization for eight putative nudix hydrolases. Evaluation of criteria for substrate identification within the Nudix family. PMID:27618147
Classification of the treble clef zinc finger: noteworthy lessons for structure and function evolution. PMID:27562564
Prediction of allosteric sites and mediating interactions through bond-to-bond propensities. PMID:27561351
Carboxylic ester hydrolases: Classification and database derived from their primary, secondary, and tertiary structures. PMID:27530203
Crystal structure of an Fe-S cluster-containing fumarate hydratase enzyme from Leishmania major reveals a unique protein fold. PMID:27528683
Did Viruses Evolve As a Distinct Supergroup from Common Ancestors of Cells? PMID:27497315
GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution. PMID:27493524
A comparison of different functions for predicted protein model quality assessment. PMID:27488386
GPU-Acceleration of Sequence Homology Searches with Database Subsequence Clustering. PMID:27482905
Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence. PMID:27472895
Quantifying Nonnative Interactions in the Protein-Folding Free-Energy Landscape. PMID:27463131
The Crystal Structure of the C-Terminal Domain of the Salmonella enterica PduO Protein: An Old Fold with a New Heme-Binding Mode. PMID:27446048
Sensing and signaling of oxidative stress in chloroplasts by inactivation of the SAL1 phosphoadenosine phosphatase. PMID:27432987
Protein-protein docking by fast generalized Fourier transforms on 5D rotational manifolds. PMID:27412858
Examination of the quality of various force fields and solvation models for the equilibrium simulations of GA88 and GB88. PMID:27392746
Evolution of the Calcium-Based Intracellular Signaling System. PMID:27358427
Sequence- and Structure-Based Analysis of Tissue-Specific Phosphorylation Sites. PMID:27332813
Landscape of protein-small ligand binding modes. PMID:27327045
Lessons from making the Structural Classification of Proteins (SCOP) and their implications for protein structure modelling. PMID:27284063
Protein rethreading: A novel approach to protein design. PMID:27229326
Advances of Proteomic Sciences in Dentistry. PMID:27187379
Coronavirus receptor switch explained from the stereochemistry of protein-carbohydrate interactions and a single mutation. PMID:27185912
Identification of a Non-Pentapeptide Region Associated with Rapid Mycobacterial Evolution. PMID:27149271
Addressing inaccuracies in BLOSUM computation improves homology search performance. PMID:27122148
The early history and emergence of molecular functions and modular scale-free network behavior. PMID:27121452
Applying PyRosetta molecular energies to separate properly oriented protein models from mirror models, obtained from contact maps. PMID:27107578
Computing the origin and evolution of the ribosome from its structure - Uncovering processes of macromolecular accretion benefiting synthetic biology. PMID:27096056
Evolutionary relationships between heme-binding ferredoxin α + β barrels. PMID:27089923
FAM46 proteins are novel eukaryotic non-canonical poly(A) polymerases. PMID:27060136
CCProf: exploring conformational change profile of proteins. PMID:27016699
Dissecting the roles of local packing density and longer-range effects in protein sequence evolution. PMID:26990194
ENTPRISE: An Algorithm for Predicting Human Disease-Associated Amino Acid Substitutions from Sequence Entropy and Predicted Protein Structures. PMID:26982818
Systems biology of the structural proteome. PMID:26969117
Structures of an all-α protein running along the DNA major groove. PMID:26939889
Classification of proteins with shared motifs and internal repeats in the ECOD database. PMID:26833690
Why reinvent the wheel? Building new proteins based on ready-made parts. PMID:26821641
Epithelial sodium channel (ENaC) family: Phylogeny, structure-function, tissue distribution, and associated inherited diseases. PMID:26772908
Evolutionary Ancestry of Eukaryotic Protein Kinases and Choline Kinases. PMID:26742849
Efficient and automated large-scale detection of structural relationships in proteins with a flexible aligner. PMID:26732380
An Amphiphysin-Like Domain in Fus2p Is Required for Rvs161p Interaction and Cortical Localization. PMID:26681517
Clusters of isoleucine, leucine, and valine side chains define cores of stability in high-energy states of globular proteins: Sequence determinants of structure and stability. PMID:26660714
An updated version of NPIDB includes new classifications of DNA-protein complexes and their families. PMID:26656949
A vocabulary of ancient peptides at the origin of folded proteins. PMID:26653858
Precise assembly of complex beta sheet topologies from de novo designed building blocks. PMID:26650357
Improving Protein Fold Recognition by Deep Learning Networks. PMID:26634993
Dealing with the Data Deluge: Handling the Multitude Of Chemical Biology Data Sources. PMID:26609498
Efficient Multicriteria Protein Structure Comparison on Modern Processor Architectures. PMID:26605332
A phylogenomic data-driven exploration of viral origins and evolution. PMID:26601271
Thyroglobulin From Molecular and Cellular Biology to Clinical Endocrinology. PMID:26595189
Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics. PMID:26555596
PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features. PMID:26553811
Revisiting the reference genomes of human pathogenic Cryptosporidium species: reannotation of C. parvum Iowa and a new C. hominis reference. PMID:26549794
FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants. PMID:26529612
Structure of AadA from Salmonella enterica: a monomeric aminoglycoside (3'')(9) adenyltransferase. PMID:26527143
PhyreStorm: A Web Server for Fast Structural Searches Against the PDB. PMID:26517951
Clustering and percolation in protein loop structures. PMID:26510704
Nucleotide binding database NBDB--a collection of sequence motifs with specific protein-ligand interactions. PMID:26507856
DynaFace: Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions Based on the Complex's Dynamics. PMID:26506003
Extending Protein Domain Boundary Predictors to Detect Discontinuous Domains. PMID:26502173
Large-scale analysis of macromolecular crowding effects on protein aggregation using a reconstituted cell-free translation system. PMID:26500644
Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes. PMID:26493560
Optimization of Expression and Purification of Recombinant Archeoglobus fulgidus F420H2:NADP+ Oxidoreductase, an F420 Cofactor Dependent Enzyme. PMID:26493287
A multi-objective optimization approach accurately resolves protein domain architectures. PMID:26458889
High-resolution structures of Lactobacillus salivarius transketolase in the presence and absence of thiamine pyrophosphate. PMID:26457526
The language of the protein universe. PMID:26451980
Event inference in multidomain families with phylogenetic reconciliation. PMID:26451642
Engineering Proteins for Thermostability with iRDP Web Server. PMID:26436543
Temporal Gene Expression Profiles of Pre Blood-Fed Adult Females Immediately Following Eclosion in the Southern House Mosquito Culex Quinquefasciatus. PMID:26435696
B1-Metallo-β-Lactamases: Where Do We Stand? PMID:26424398
The Recognition of Identical Ligands by Unrelated Proteins. PMID:26421501
Comparison of the Internal Dynamics of Metalloproteases Provides New Insights on Their Function and Evolution. PMID:26397984
Control over overall shape and size in de novo designed proteins. PMID:26396255
Structural Bridges through Fold Space. PMID:26372166
The value of protein structure classification information-Surveying the scientific literature. PMID:26313554
Weak conservation of structural features in the interfaces of homologous transient protein-protein complexes. PMID:26311309
CoMOGrad and PHOG: From Computer Vision to Fast and Accurate Protein Tertiary Structure Retrieval. PMID:26293226
Structure-Based Phylogenetic Analysis of the Lipocalin Superfamily. PMID:26263546
The organization of domains in proteins obeys Menzerath-Altmann's law of language. PMID:26260760
Systematic analyses reveal uniqueness and origin of the CFEM domain in fungi. PMID:26255557
The history of the CATH structural classification of protein domains. PMID:26253692
Structure of the human MLH1 N-terminus: implications for predisposition to Lynch syndrome. PMID:26249686
Protonation of Glu(135) Facilitates the Outward-to-Inward Structural Transition of Fucose Transporter. PMID:26244736
Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2. PMID:26231283
De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods. PMID:26228684
Mitochondrial genomes are retained by selective constraints on protein targeting. PMID:26195779
Structural Bioinformatics Inspection of neXtProt PE5 Proteins in the Human Proteome. PMID:26193931
The UBR-box and its relationship to binuclear RING-like treble clef zinc fingers. PMID:26185100
A hybrid method for protein-protein interface prediction. PMID:26178156
Structure alignment of membrane proteins: Accuracy of available tools and a consensus strategy. PMID:26178143
A composite double-/single-stranded RNA-binding region in protein Prp3 supports tri-snRNP stability and splicing. PMID:26161500
Functional classification of CATH superfamilies: a domain-based approach for protein function annotation. PMID:26139634
Ambiguity and variability of database and software names in bioinformatics. PMID:26131352
Structural and Biochemical Characterization of AidC, a Quorum-Quenching Lactonase with Atypical Selectivity. PMID:26115006
Choline Acetyltransferase Mutations Causing Congenital Myasthenic Syndrome: Molecular Findings and Genotype-Phenotype Correlations. PMID:26080897
Structural Studies of the HIV-1 Integrase Protein: Compound Screening and Characterization of a DNA-Binding Inhibitor. PMID:26046987
On Learning and Visualizing Practice-based Clinical Pathways for Chronic Kidney Disease. PMID:25954471
Customised fragments libraries for protein structure prediction based on structural class annotations. PMID:25925397
Manual classification strategies in the ECOD database. PMID:25917548
A virtual pebble game to ensemble average graph rigidity. PMID:25904973
Building a better fragment library for de novo protein structure prediction. PMID:25901595
The response of Greek key proteins to changes in connectivity depends on the nature of their secondary structure. PMID:25861761
A structure-based classification and analysis of protein domain family binding sites and their interactions. PMID:25860777
Domain-swapped dimer of Pseudomonas aeruginosa cytochrome c551: structural insights into domain swapping of cytochrome c family proteins. PMID:25853415
CHOPIN: a web resource for the structural and functional proteome of Mycobacterium tuberculosis. PMID:25833954
StaRProtein, a web server for prediction of the stability of repeat proteins. PMID:25807112
Structural characterization of substrate and inhibitor binding to farnesyl pyrophosphate synthase from Pseudomonas aeruginosa. PMID:25760619
Application of data mining tools for classification of protein structural class from residue based averaged NMR chemical shifts. PMID:25758094
How do disordered regions achieve comparable functions to structured domains? PMID:25752799
A new method to improve network topological similarity search: applied to fold recognition. PMID:25717198
Algorithmic approaches to protein-protein interaction site prediction. PMID:25713596
Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses. PMID:25673291
Molecular and evolutionary insights into the structural organization of cation chloride cotransporters. PMID:25653592
Novel mutations confirm that COL11A2 is responsible for autosomal recessive non-syndromic hearing loss DFNB53. PMID:25633957
The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam. PMID:25614388
Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification. PMID:25573913
MUFOLD-DB: a processed protein structure database for protein structure prediction and analysis. PMID:25559128
A three dimensional visualisation approach to protein heavy-atom structure reconstruction. PMID:25551190
Structure based annotation of Helicobacter pylori strain 26695 proteome. PMID:25549250
Identifying tandem Ankyrin repeats in protein structures. PMID:25547411
WEBnm@ v2.0: Web server and services for comparing protein flexibility. PMID:25547242
Refinement by shifting secondary structure elements improves sequence alignments. PMID:25546158
Protein inter-domain linker prediction using Random Forest and amino acid physiochemical properties. PMID:25521329
Bhageerath-H: a homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins. PMID:25521245
A geometric clustering algorithm with applications to structural data. PMID:25517067
NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. PMID:25505092
Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. PMID:25503938
Contribution of anion-π interactions to the stability of Sm/LSm proteins. PMID:25502146
Overexpression of penicillin V acylase from Streptomyces lavendulae and elucidation of its catalytic residues. PMID:25501472
Structural templates for comparative protein docking. PMID:25488330
On the role of physics and evolution in dictating protein structure and function. PMID:25484448
ECOD: an evolutionary classification of protein domains. PMID:25474468
The amino acid alphabet and the architecture of the protein sequence-structure map. I. Binary alphabets. PMID:25473967
Operator recognition by the ROK transcription factor family members, NagC and Mlc. PMID:25452338
Utilization of paramagnetic relaxation enhancements for high-resolution NMR structure determination of a soluble loop-rich protein with sparse NOE distance restraints. PMID:25428765
The SUPERFAMILY 1.75 database in 2014: a doubling of data. PMID:25414345
Early chordate origin of the vertebrate integrin αI domains. PMID:25409021
Contribution of cation-π interactions to the stability of Sm/LSm oligomeric assemblies. PMID:25408427
Improvements to REDCRAFT: a software tool for simultaneous characterization of protein backbone structure and dynamics from residual dipolar couplings. PMID:25403759
Characteristics of protein residue-residue contacts and their application in contact prediction. PMID:25374390
A census of human RNA-binding proteins. PMID:25365966
dcGOR: an R package for analysing ontologies and protein domain annotations. PMID:25356683
Improving protein fold recognition by random forest. PMID:25350499
SbnG, a citrate synthase in Staphylococcus aureus: a new fold on an old enzyme. PMID:25336653
A calibrated chronology of biochemistry reveals a stem line of descent responsible for planetary biodiversity. PMID:25309572
TERPRED: A Dynamic Structural Data Analysis Tool. PMID:25302339
Improving contact prediction along three dimensions. PMID:25299132
Use of a structural alphabet to find compatible folds for amino acid sequences. PMID:25297700
The intrinsically disordered regions of the Drosophila melanogaster Hox protein ultrabithorax select interacting proteins based on partner topology. PMID:25286318
Streptomyces coelicolor SCO4226 is a nickel binding protein. PMID:25285530
NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection. PMID:25262355
A method of protein model classification and retrieval using bag-of-visual-features. PMID:25258644
Differential effects of a mutation on the normal and promiscuous activities of orthologs: implications for natural and directed evolution. PMID:25246702
How a spatial arrangement of secondary structure elements is dispersed in the universe of protein folds. PMID:25243952
Crystal structure of a conserved hypothetical protein MJ0927 from Methanocaldococcus jannaschii reveals a novel quaternary assembly in the Nif3 family. PMID:25243119
Integrative visual analysis of protein sequence mutations. PMID:25237389
eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models. PMID:25232727
Neighbor preferences of amino acids and context-dependent effects of amino acid substitutions in human, mouse, and dog. PMID:25210846
Evolutionary conservation and expression of human RNA-binding proteins and their role in human genetic disease. PMID:25201102
Effects of light and the regulatory B-subunit composition of protein phosphatase 2A on the susceptibility of Arabidopsis thaliana to aphid (Myzus persicae) infestation. PMID:25191331
Biophysics of protein evolution and evolutionary protein biophysics. PMID:25165599
A tree of cellular life inferred from a genomic census of molecular functions. PMID:25128982
Local packing density is the main structural determinant of the rate of protein sequence evolution at site level. PMID:25121105
Exploring representations of protein structure for automated remote homology detection and mapping of protein structure space. PMID:25080993
Global view of the protein universe. PMID:25071170
The structure and specificity of the type III secretion system effector NleC suggest a DNA mimicry mechanism of substrate recognition. PMID:25040221
Evolutionary relationship of two ancient protein superfolds. PMID:25038785
Identification of an ideal-like fingerprint for a protein fold using overlapped conserved residues based approach. PMID:25008052
A phylogenetic analysis of the ubiquitin superfamily based on sequence and structural information. PMID:24997693
Structure of a new DNA-binding domain which regulates pathogenesis in a wide variety of fungi. PMID:24994900
Archaea: the first domain of diversified life. PMID:24987307
Small molecule inhibitors of HCV replication from pomegranate. PMID:24958333
Identification of promiscuous ene-reductase activity by mining structural databases using active site constellations. PMID:24954722
A model-based information sharing protocol for profile Hidden Markov Models used for HIV-1 recombination detection. PMID:24946781
Solution NMR structures of homeodomains from human proteins ALX4, ZHX1, and CASP8AP2 contribute to the structural coverage of the Human Cancer Protein Interaction Network. PMID:24941917
Features of large hinge-bending conformational transitions. Prediction of closed structure from open state. PMID:24940783
Efficient design of meganucleases using a machine learning approach. PMID:24934562
Structural insights into SraP-mediated Staphylococcus aureus adhesion to host cells. PMID:24901708
Predicted structure and domain organization of rotavirus capping enzyme and innate immune antagonist VP3. PMID:24899176
Sequence analysis on the information of folding initiation segments in ferredoxin-like fold proteins. PMID:24884463
Computational prediction of protein function based on weighted mapping of domains and GO terms. PMID:24868539
The natural history of transfer RNA and its interactions with the ribosome. PMID:24847358
Multiple functional roles of the accessory I-domain of bacteriophage P22 coat protein revealed by NMR structure and CryoEM modeling. PMID:24836025
Structure of a sedoheptulose 7-phosphate cyclase: ValA from Streptomyces hygroscopicus. PMID:24832673
Origin and evolution of the sodium -pumping NADH: ubiquinone oxidoreductase. PMID:24809444
SymD webserver: a platform for detecting internally symmetric protein structures. PMID:24799435
Classification of intrinsically disordered regions and proteins. PMID:24773235
Elastic network models capture the motions apparent within ensembles of RNA structures. PMID:24759093
From local structure to a global framework: recognition of protein folds. PMID:24740960
Intermolecular β-strand networks avoid hub residues and favor low interconnectedness: a potential protection mechanism against chain dissociation upon mutation. PMID:24733378
Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms. PMID:24710297
3PFDB+: improved search protocol and update for the identification of representatives of protein sequence domain families. PMID:24700812
Coevolution signals capture the specific packing of secondary structures in protein architecture. PMID:24699983
Mutational and crystallographic analysis of l-amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813: Interconversion between oxidase and monooxygenase activities. PMID:24693490
The evolution of human cells in terms of protein innovation. PMID:24692656
Structure-based Methods for Computational Protein Functional Site Prediction. PMID:24688745
Ramachandran analysis of conserved glycyl residues in homologous proteins of known structure. PMID:24687432
Systematic detection of internal symmetry in proteins using CE-Symm. PMID:24681267
MRFalign: protein homology detection through alignment of Markov random fields. PMID:24675572
Structural similarity between defense peptide from wheat and scorpion neurotoxin permits rational functional design. PMID:24671422
Improved transcript isoform discovery using ORF graphs. PMID:24659106
Prediction of RNA binding residues: an extensive analysis based on structure and function to select the best predictor. PMID:24658593
Protein fold recognition using geometric kernel data fusion. PMID:24590441
Improvement in low-homology template-based modeling by employing a model evaluation method with focus on topology. PMID:24587135
Proposing a highly accurate protein structural class predictor using segmentation-based features. PMID:24564476
The HicA toxin from Burkholderia pseudomallei has a role in persister cell formation. PMID:24502667
Global patterns of protein domain gain and loss in superkingdoms. PMID:24499935
Structure to function prediction of hypothetical protein KPN_00953 (Ycbk) from Klebsiella pneumoniae MGH 78578 highlights possible role in cell wall metabolism. PMID:24499172
Energetic frustrations in protein folding at residue resolution: a homologous simulation study of Im9 proteins. PMID:24498176
Comparative analysis of proteomes and functionomes provides insights into origins of cellular diversification. PMID:24492748
Improving predictions of protein-protein interfaces by combining amino acid-specific classifiers based on structural and physicochemical descriptors with their weighted neighbor averages. PMID:24489849
Enzyme recruitment and its role in metabolic expansion. PMID:24483367
Parallel implementation of 3D protein structure similarity searches using a GPU and the CUDA. PMID:24481593
Tracking molecular recognition at the atomic level with a new protein scaffold based on the OB-fold. PMID:24465865
Quantitative characterization of protein tertiary motifs. PMID:24464316
BurrH: a new modular DNA binding protein for genome engineering. PMID:24452192
Kinks, loops, and protein folding, with protein A as an example. PMID:24437917
Quantitative theory of hydrophobic effect as a driving force of protein structure. PMID:24408023
Highly reinforced structure of a C-terminal dimerization domain in von Willebrand factor. PMID:24394662
Atlas of coronavirus replicase structure. PMID:24355834
Structural propensities of human ubiquitination sites: accessibility, centrality and local conformation. PMID:24349449
Exploring early stages of the chemical unfolding of proteins at the proteome scale. PMID:24348236
Identifying RNA-binding residues based on evolutionary conserved structural and energetic features. PMID:24343026
Sequence-based Gaussian network model for protein dynamics. PMID:24336646
MMDB and VAST+: tracking structural similarities between macromolecular complexes. PMID:24319143
Sequence, biophysical, and structural analyses of the PstS lipoprotein (BB0215) from Borrelia burgdorferi reveal a likely binding component of an ABC-type phosphate transporter. PMID:24318969
Multilevel structural characteristics for the natural substrate proteins of bacterial small heat shock proteins. PMID:24318917
5-Methylation of cytosine in CG:CG base-pair steps: a physicochemical mechanism for the epigenetic control of DNA nanomechanics. PMID:24313757
SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures. PMID:24304899
SCOP2 prototype: a new approach to protein structure mining. PMID:24293656
mCSM: predicting the effects of mutations in proteins using graph-based signatures. PMID:24281696
LUD, a new protein domain associated with lactate utilization. PMID:24274019
Structure-based function prediction of uncharacterized protein using binding sites comparison. PMID:24244144
Exploring fold space preferences of new-born and ancient protein superfamilies. PMID:24244135
The crystal structure of sterol carrier protein 2 from Yarrowia lipolytica and the evolutionary conservation of a large, non-specific lipid-binding cavity. PMID:24241823
Structural updates of alignment of protein domains and consequences on evolutionary models of domain superfamilies. PMID:24237883
Folding properties of cytosine monophosphate kinase from E. coli indicate stabilization through an additional insert in the NMP binding domain. PMID:24205218
LenVarDB: database of length-variant protein domains. PMID:24194591
Molecular replacement then and now. PMID:24189239
Improved estimates of coordinate error for molecular replacement. PMID:24189232
Comparative analysis of barophily-related amino acid content in protein domains of Pyrococcus abyssi and Pyrococcus furiosus. PMID:24187517
Defining structural and evolutionary modules in proteins: a community detection approach to explore sub-domain architecture. PMID:24131821
A horizontal alignment tool for numerical trend discovery in sequence data: application to protein hydropathy. PMID:24130469
FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking. PMID:24130308
Structure and function of a novel LD-carboxypeptidase a involved in peptidoglycan recycling. PMID:24123814
Tyrosyl radicals in dehaloperoxidase: how nature deals with evolving an oxygen-binding globin to a biologically relevant peroxidase. PMID:24100039
Oligomerization interface of RAGE receptor revealed by MS-monitored hydrogen deuterium exchange. PMID:24098480
3did: a catalog of domain-based interactions of known three-dimensional structure. PMID:24081580
An empirical test of convergent evolution in rhodopsins. PMID:24077848
Rebelling for a reason: protein structural "outliers". PMID:24073209
Human cytomegalovirus gene UL76 induces IL-8 expression through activation of the DNA damage response. PMID:24068928
Towards comprehensive analysis of protein family quantitative stability-flexibility relationships using homology models. PMID:24061925
Structure of the Mtb CarD/RNAP β-lobes complex reveals the molecular basis of interaction and presents a distinct DNA-binding domain for Mtb CarD. PMID:24055315
Structures of human primase reveal design of nucleotide elongation site and mode of Pol α tethering. PMID:24043831
Protein similarity networks reveal relationships among sequence, structure, and function within the Cupin superfamily. PMID:24040257
Systematic mutational analysis of the putative hydrolase PqsE: toward a deeper molecular understanding of virulence acquisition in Pseudomonas aeruginosa. PMID:24040042
A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction. PMID:24018415
Structure homology and interaction redundancy for discovering virus-host protein interactions. PMID:24008843
Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility. PMID:23991065
Structure of isochorismate synthase DhbC from Bacillus anthracis. PMID:23989140
Octarellin VI: using rosetta to design a putative artificial (β/α)8 protein. PMID:23977165
Protein structure validation and identification from unassigned residual dipolar coupling data using 2D-PDPA. PMID:23973992
Protein domain definition should allow for conditional disorder. PMID:23963781
A 3-dimensional trimeric β-barrel model for Chlamydia MOMP contains conserved and novel elements of Gram-negative bacterial porins. PMID:23935908
Exhaustive comparison and classification of ligand-binding surfaces in proteins. PMID:23934772
Anti-viral immune responses in a primitive lung: characterization and expression analysis of interferon-inducible immunoproteasome subunits LMP2, LMP7 and MECL-1 in a sarcopterygian fish, the Nigerian spotted lungfish (Protopterus dolloi). PMID:23932981
How old is my gene? PMID:23915718
Relocating the active-site lysine in rhodopsin and implications for evolution of retinylidene proteins. PMID:23904486
β-Bulges: extensive structural analyses of β-sheets irregularities. PMID:23904395
Crystal structure of α-1,4-glucan lyase, a unique glycoside hydrolase family member with a novel catalytic mechanism. PMID:23902768
Prediction of RNA binding proteins comes of age from low resolution to high resolution. PMID:23872922
Putative osmosensor--OsHK3b--a histidine kinase protein from rice shows high structural conservation with its ortholog AtHK1 from Arabidopsis. PMID:23869567
DoSA: Database of Structural Alignments. PMID:23846594
PFClust: a novel parameter free clustering algorithm. PMID:23819480
Evaluating template-based and template-free protein-protein complex structure prediction. PMID:23818491
Compressive genomics for protein databases. PMID:23812995
ThreaDom: extracting protein domain boundary information from multiple threading alignments. PMID:23812990
Novel approach for selecting the best predictor for identifying the binding sites in DNA binding proteins. PMID:23788679
The structure of latherin, a surfactant allergen protein from horse sweat and saliva. PMID:23782536
bioNerDS: exploring bioinformatics' database and software use through literature mining. PMID:23768135
Characterizing protein domain associations by Small-molecule ligand binding. PMID:23745168
Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment. PMID:23719418
T-RMSD: a web server for automated fine-grained protein structural classification. PMID:23716642
Human prostatic acid phosphatase: structure, function and regulation. PMID:23698773
Efficient protein structure search using indexing methods. PMID:23691543
Helical ambivalency induced by point mutations. PMID:23675772
Rapid catalytic template searching as an enzyme function prediction procedure. PMID:23675414
Large-scale modelling of the divergent spectrin repeats in nesprins: giant modular proteins. PMID:23671687
Comparison study on statistical features of predicted secondary structures for protein structural class prediction: From content to position. PMID:23641706
Chapter 15: disease gene prioritization. PMID:23633938
The four-transmembrane protein IP39 of Euglena forms strands by a trimeric unit repeat. PMID:23612307
Identification and characterization of a previously undescribed family of sequence-specific DNA-binding domains. PMID:23610392
Crystal and solution studies reveal that the transcriptional regulator AcnR of Corynebacterium glutamicum is regulated by citrate-Mg2+ binding to a non-canonical pocket. PMID:23589369
Recurrent structural motifs in non-homologous protein structures. PMID:23574940
Structure and function of the DUF2233 domain in bacteria and in the human mannose 6-phosphate uncovering enzyme. PMID:23572527
Origin and evolution of protein fold designs inferred from phylogenomic analysis of CATH domain structures in proteomes. PMID:23555236
Viral evolution: Primordial cellular origins and late adaptation to parasitism. PMID:23550145
Local network patterns in protein-protein interfaces. PMID:23520460
Structural phylogenomics reveals gradual evolutionary replacement of abiotic chemistries by protein enzymes in purine metabolism. PMID:23516625
Sequence and structural characterization of Trx-Grx type of monothiol glutaredoxins from Ashbya gossypii. PMID:23515490
Function prediction from networks of local evolutionary similarity in protein structure. PMID:23514548
Protein structure alignment beyond spatial proximity. PMID:23486213
Alignment of helical membrane protein sequences using AlignMe. PMID:23469223
Increasing sequence search sensitivity with transitive alignments. PMID:23457449
A general framework of persistence strategies for biological systems helps explain domains of life. PMID:23443991
Highly abundant proteins favor more stable 3D structures in yeast. PMID:23442924
Inherent relationships among different biophysical prediction methods for intrinsically disordered proteins. PMID:23442871
Exploring angular distance in protein-protein docking algorithms. PMID:23437194
Hierarchical classification of protein folds using a novel ensemble classifier. PMID:23437146
Improved detection of remote homologues using cascade PSI-BLAST: influence of neighbouring protein families on sequence coverage. PMID:23437136
Local conformational changes in the DNA interfaces of proteins. PMID:23418514
Pseudomonas aeruginosa PA1006 is a persulfide-modified protein that is critical for molybdenum homeostasis. PMID:23409003
Viral capsid proteins are segregated in structural fold space. PMID:23408879
Microsecond folding experiments and simulations: a match is made. PMID:23361200
Evolutionary optimization of protein folding. PMID:23341762
Evolutionary conservation of the polyproline II conformation surrounding intrinsically disordered phosphorylation sites. PMID:23341186
MICAN: a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, C(α) only models, Alternative alignments, and Non-sequential alignments. PMID:23331634
Eukaryotic GPN-loop GTPases paralogs use a dimeric assembly reminiscent of archeal GPN. PMID:23324351
Molecular modeling comparison of the performance of NS5b polymerase inhibitor (PSI-7977) on prevalent HCV genotypes. PMID:23322006
Self consistency grouping: a stringent clustering method. PMID:23320864
Binding pocket optimization by computational protein design. PMID:23300688
A universal trend among proteomes indicates an oily last common ancestor. PMID:23300421
Structural and functional insights into (S)-ureidoglycolate dehydrogenase, a metabolic branch point enzyme in nitrogen utilization. PMID:23284870
Interaction signatures stabilizing the NAD(P)-binding Rossmann fold: a structure network approach. PMID:23284738
Mapping small molecule binding data to structural domains. PMID:23282026
Beyond BLASTing: tertiary and quaternary structure analysis helps identify major vault proteins. PMID:23275487
Structural and functional analysis of multi-interface domains. PMID:23272073
Golden triangle for folding rates of globular proteins. PMID:23251035
Conservation of the three-dimensional structure in non-homologous or unrelated proteins. PMID:23244440
What can we learn from the evolution of protein-ligand interactions to aid the design of new therapeutics? PMID:23240060
A global comparison of the human and T. brucei degradomes gives insights about possible parasite drug targets. PMID:23236535
Structure and dynamics of a primordial catalytic fold generated by in vitro evolution. PMID:23222886
Identification of nucleotide-binding sites in protein structures: a novel approach based on nucleotide modularity. PMID:23209685
D²P²: database of disordered protein predictions. PMID:23203878
The RCSB Protein Data Bank: new resources for research and education. PMID:23193259
Defining and predicting structurally conserved regions in protein superfamilies. PMID:23193223
Structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC118. PMID:23192019
eThread: a highly optimized machine learning-based approach to meta-threading and the modeling of protein tertiary structures. PMID:23185577
An artificial neural network approach to improving the correlation between protein energetics and the backbone structure. PMID:23184572
Counterbalance of ligand- and self-coupled motions characterizes multispecificity of ubiquitin. PMID:23169174
Solution NMR structure of the helicase associated domain BVU_0683(627-691) from Bacteroides vulgatus provides first structural coverage for protein domain family PF03457 and indicates domain binding to DNA. PMID:23160728
Crowding, molecular volume and plasticity: an assessment involving crystallography, NMR and simulations. PMID:23151785
Structural modelling and mutant cycle analysis predict pharmacoresponsiveness of a Na(V)1.7 mutant channel. PMID:23149731
Assessing predictors of changes in protein stability upon mutation using self-consistency. PMID:23144695
The genome of the obligate intracellular parasite Trachipleistophora hominis: new insights into microsporidian genome dynamics and reductive evolution. PMID:23133373
Identifying structural domains of proteins using clustering. PMID:23116496
Enzyme informatics. PMID:23116471
When a domain is not a domain, and why it is important to properly filter proteins in databases: conflicting definitions and fold classification systems for structural domains make filtering of such databases imperative. PMID:23108912
Assessing the accuracy of template-based structure prediction metaservers by comparison with structural genomics structures. PMID:23086054
Evolutionarily consistent families in SCOP: sequence, structure and function. PMID:23078280
Solution structure, copper binding and backbone dynamics of recombinant Ber e 1-the major allergen from Brazil nut. PMID:23056307
Random field model reveals structure of the protein recombinational landscape. PMID:23055915
Insilico analysis and molecular docking of resuscitation promoting factor B (RpfB) protein of Mycobacterium tuberculosis. PMID:23055604
A novel neural response algorithm for protein function prediction. PMID:23046521
MESSA: MEta-Server for protein Sequence Analysis. PMID:23031578
Structure and assembly of a trans-periplasmic channel for type IV pili in Neisseria meningitidis. PMID:23028322
Quality assessment of protein model-structures based on structural and functional similarities. PMID:22998498
A modular perspective of protein structures: application to fragment based loop modeling. PMID:22987351
Computational design of a Diels-Alderase from a thermophilic esterase: the importance of dynamics. PMID:22983490
Benefits of using molecular structure and abundance in phylogenomic analysis. PMID:22973296
TFinDit: transcription factor-DNA interaction data depository. PMID:22943312
Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB. PMID:22942020
Selective constraint on human pre-mRNA splicing by protein structural properties. PMID:22936073
Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network in Thermotoga maritima. PMID:22925190
Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya. PMID:22920653
Subcellular localization of extracytoplasmic proteins in monoderm bacteria: rational secretomics-based strategy for genomic and proteomic analyses. PMID:22912771
PACSY, a relational database management system for protein structure and chemical shift analysis. PMID:22903636
Biphasic patterns of diversification and the emergence of modules. PMID:22891076
Dynamic features of homodimer interfaces calculated by normal-mode analysis. PMID:22887034
Supervised protein family classification and new family construction. PMID:22876787
Deep architectures for protein contact map prediction. PMID:22847931
Molecular and biochemical analyses of the GH44 module of CbMan5B/Cel44A, a bifunctional enzyme from the hyperthermophilic bacterium Caldicellulosiruptor bescii. PMID:22843537
Three structural representatives of the PF06855 protein domain family from Staphyloccocus aureus and Bacillus subtilis have SAM domain-like folds and different functions. PMID:22843344
Coexistence of phases in a protein heterodimer. PMID:22830730
Defining and searching for structural motifs using DeepView/Swiss-PdbViewer. PMID:22823337
Predictive sequence analysis of the Candidatus Liberibacter asiaticus proteome. PMID:22815919
Template-based protein structure modeling using the RaptorX web server. PMID:22814390
Crystal structure of the conserved domain of the DC lysosomal associated membrane protein: implications for the lysosomal glycocalyx. PMID:22809326
Structural and biochemical characterization of phage λ FI protein (gpFI) reveals a novel mechanism of DNA packaging chaperone activity. PMID:22801427
Re-visiting protein-centric two-tier classification of existing DNA-protein complexes. PMID:22800292
GFam: a platform for automatic annotation of gene families. PMID:22790981
Predicting new indications for approved drugs using a proteochemometric method. PMID:22780961
CbrA is a flavin adenine dinucleotide protein that modifies the Escherichia coli outer membrane and confers specific resistance to Colicin M. PMID:22773789
Structure-function analysis of human TYW2 enzyme required for the biosynthesis of a highly modified Wybutosine (yW) base in phenylalanine-tRNA. PMID:22761755
Computing the protein binding sites. PMID:22759425
Local structural differences in homologous proteins: specificities in different SCOP classes. PMID:22745680
Prediction of metal ion-binding sites in proteins using the fragment transformation method. PMID:22723976
Accurate prediction of protein structural class. PMID:22723837
Prediction of protein domain with mRMR feature selection and analysis. PMID:22720092
How many protein-protein interactions types exist in nature? PMID:22719985
Self-complementarity within proteins: bridging the gap between binding and folding. PMID:22713576
BioShell Threader: protein homology detection based on sequence profiles and secondary structure profiles. PMID:22693216
Cysteine-rich domains related to Frizzled receptors and Hedgehog-interacting proteins. PMID:22693159
New finite-size correction for local alignment score distributions. PMID:22691307
PBSword: a web server for searching similar protein-protein binding sites. PMID:22689645
PSC: protein surface classification. PMID:22669905
SAS-Pro: simultaneous residue assignment and structure superposition for protein structure alignment. PMID:22662161
Computer-aided antibody design. PMID:22661385
Exploring the evolution of protein function in Archaea. PMID:22646318
Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. PMID:22638584
A thermodynamic definition of protein domains. PMID:22635268
Extent of structural asymmetry in homodimeric proteins: prevalence and relevance. PMID:22629324
Insights into the fold organization of TIM barrel from interaction energy based structure networks. PMID:22615547
Global analysis of chaperone effects using a reconstituted cell-free translation system. PMID:22615364
ProDis-ContSHC: learning protein dissimilarity measures and hierarchical context coherently for protein-protein comparison in protein database retrieval. PMID:22594999
Structural bioinformatics of the human spliceosomal proteome. PMID:22573172
Evolution of oligomeric state through geometric coupling of protein interfaces. PMID:22566652
Transmembrane helix: simple or complex. PMID:22564899
Mapping the Anopheles gambiae odorant binding protein 1 (AgamOBP1) using modeling techniques, site directed mutagenesis, circular dichroism and ligand binding assays. PMID:22564768
Clusters of ancestrally related genes that show paralogy in whole or in part are a major feature of the genomes of humans and other species. PMID:22563380
Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins. PMID:22554255
Bioinformatics and variability in drug response: a protein structural perspective. PMID:22552919
Fitting hidden Markov models of protein domains to a target species: application to Plasmodium falciparum. PMID:22548871
Computational structural analysis of proteins of Mycobacterium tuberculosis and a resource for identifying off-targets. PMID:22538508
Exploring functionally related enzymes using radially distributed properties of active sites around the reacting points of bound ligands. PMID:22536854
Use of structural phylogenetic networks for classification of the ferritin-like superfamily. PMID:22535960
HD-RNAS: An Automated Hierarchical Database of RNA Structures. PMID:22529851
Domain enhanced lookup time accelerated BLAST. PMID:22510480
Boosting Protein Threading Accuracy. PMID:22506254
Beta-strand interfaces of non-dimeric protein oligomers are characterized by scattered charged residue patterns. PMID:22496732
Energetic selection of topology in ferredoxins. PMID:22496635
Multicopper oxidase-3 is a laccase associated with the peritrophic matrix of Anopheles gambiae. PMID:22479493
Functional repertoire, molecular pathways and diseases associated with 3D domain swapping in the human proteome. PMID:22472218
Roles of residues in the interface of transient protein-protein complexes before complexation. PMID:22451863
A structural model of the E. coli PhoB dimer in the transcription initiation complex. PMID:22433509
Ribosomal history reveals origins of modern protein synthesis. PMID:22427882
β-sheet topology prediction with high precision and recall for β and mixed α/β proteins. PMID:22427840
Solution NMR structure of the ribosomal protein RP-L35Ae from Pyrococcus furiosus. PMID:22422653
Retrieving backbone string neighbors provides insights into structural modeling of membrane proteins. PMID:22415040
The evolution of filamin-a protein domain repeat perspective. PMID:22414427
Comparative modeling and protein-like features of hydrophobic-polar models on a two-dimensional lattice. PMID:22411636
SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone. PMID:22408192
Text mining improves prediction of protein functional sites. PMID:22393388
Identification of potential drug targets implicated in Parkinson's disease from human genome: insights of using fused domains in hypothetical proteins as probes. PMID:22389811
Calculating ensemble averaged descriptions of protein rigidity without sampling. PMID:22383947
Cutoff Scanning Matrix (CSM): structural classification and function prediction by protein inter-residue distance patterns. PMID:22369665
Accommodation of profound sequence differences at the interfaces of eubacterial RNA polymerase multi-protein assembly. PMID:22359428
Stability of domain structures in multi-domain proteins. PMID:22355559
Crystal structure of a putative isochorismatase hydrolase from Oleispira antarctica. PMID:22350524
Composite structural motifs of binding sites for delineating biological functions of proteins. PMID:22347478
The plant proteome folding project: structure and positive selection in plant protein families. PMID:22345424
The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms. PMID:22284070
KB-Rank: efficient protein structure and functional annotation identification via text query. PMID:22270457
ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures. PMID:22268964
Cloning, Baeyer-Villiger biooxidations, and structures of the camphor pathway 2-oxo-Δ(3)-4,5,5-trimethylcyclopentenylacetyl-coenzyme A monooxygenase of Pseudomonas putida ATCC 17453. PMID:22267661
Convergent evolution in structural elements of proteins investigated using cross profile analysis. PMID:22244085
Characterisation of a cell wall-anchored protein of Staphylococcus saprophyticus associated with linoleic acid resistance. PMID:22243671
Solution NMR of a 463-residue phosphohexomutase: domain 4 mobility, substates, and phosphoryl transfer defect. PMID:22242625
Classification of protein functional surfaces using structural characteristics. PMID:22238424
C7orf30 is necessary for biogenesis of the large subunit of the mitochondrial ribosome. PMID:22238376
Prediction of protein-protein binding free energies. PMID:22238219
Cis-trans peptide variations in structurally similar proteins. PMID:22227866
The phylogenomic roots of modern biochemistry: origins of proteins, cofactors and protein biosynthesis. PMID:22210458
The natural history of ubiquitin and ubiquitin-related domains. PMID:22201813
Kinetic properties of alternatively spliced isoforms of laccase-2 from Tribolium castaneum and Anopheles gambiae. PMID:22198355
Solution NMR structures reveal a distinct architecture and provide first structures for protein domain family PF04536. PMID:22198206
Structural constraints on the covariance matrix derived from multiple aligned protein sequences. PMID:22194819
Detection of secondary and supersecondary structures of proteins from cryo-electron microscopy. PMID:22186625
The relationship between proteome size, structural disorder and organism complexity. PMID:22182830
Active site detection by spatial conformity and electrostatic analysis--unravelling a proteolytic function in shrimp alkaline phosphatase. PMID:22174814
Biophysical and structural considerations for protein sequence evolution. PMID:22171550
SProt: sphere-based protein structure similarity algorithm. PMID:22166105
PSS-3D1D: an improved 3D1D profile method of protein fold recognition for the annotation of twilight zone sequences. PMID:22160493
Structural and functional analysis of the archaeal endonuclease Nob1. PMID:22156373
Statistical significance of threading scores. PMID:22149633
Accessible surfaces of beta proteins increase with increasing protein molecular mass more rapidly than those of other proteins. PMID:22145047
SitEx: a computer system for analysis of projections of protein functional sites on eukaryotic genes. PMID:22139920
The Pfam protein families database. PMID:22127870
Dimensionality reduction in computational demarcation of protein tertiary structures. PMID:22116606
Protein domain of unknown function 3233 is a translocation domain of autotransporter secretory mechanism in gamma proteobacteria. PMID:22073138
Structural annotation of Mycobacterium tuberculosis proteome. PMID:22073123
Divergence and convergence in enzyme evolution. PMID:22069324
CONTSOR--a new knowledge-based fold recognition potential, based on side chain orientation and contacts between residue terminal groups. PMID:22057923
Crystal structure of the predicted phospholipase LYPLAL1 reveals unexpected functional plasticity despite close relationship to acyl protein thioesterases. PMID:22052940
Elucidation of the ATP7B N-domain Mg2+-ATP coordination site and its allosteric regulation. PMID:22046264
Benchmarks for flexible and rigid transcription factor-DNA docking. PMID:22044637
Minimal functional sites allow a classification of zinc sites in proteins. PMID:22043316
STRIKE: evaluation of protein MSAs using a single 3D structure. PMID:22039207
Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins. PMID:22024092
Conservation of the human integrin-type beta-propeller domain in bacteria. PMID:22022374
Structure and mechanisms of Escherichia coli aspartate transcarbamoylase. PMID:22011033
Using structure to explore the sequence alignment space of remote homologs. PMID:21998567
CASP9 target classification. PMID:21997778
Evolution of vacuolar proton pyrophosphatase domains and volutin granules: clues into the early evolutionary origin of the acidocalcisome. PMID:21974828
Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction. PMID:21955494
Binding leverage as a molecular basis for allosteric regulation. PMID:21935347
Discovery of the first insect nidovirus, a missing evolutionary link in the emergence of the largest RNA virus genomes. PMID:21931546
A graph-based clustering method applied to protein sequences. PMID:21927545
Prediction of functionally important residues in globular proteins from unusual central distances of amino acids. PMID:21923943
Classification of heterodimer interfaces using docking models and construction of scoring functions for the complex structure prediction. PMID:21918618
Evaluating the efficacy of a structure-derived amino acid substitution matrix in detecting protein homologs by BLAST and PSI-BLAST. PMID:21918617
Discrimination between biological interfaces and crystal-packing contacts. PMID:21918609
Defense islands in bacterial and archaeal genomes and prediction of novel defense systems. PMID:21908672
Mycobacteriophage genome database. PMID:21904429
Evolution at the subgene level: domain rearrangements in the Drosophila phylogeny. PMID:21900599
Characterizing protein motions from structure. PMID:21893421
Conservation of the C-type lectin fold for massive sequence variation in a Treponema diversity-generating retroelement. PMID:21873231
Cross-Genome Comparisons of Newly Identified Domains in Mycoplasma gallisepticum and Domain Architectures with Other Mycoplasma species. PMID:21860605
Comprehensive structural and substrate specificity classification of the Saccharomyces cerevisiae methyltransferome. PMID:21858014
A crystal structure of the catalytic core domain of an avian sarcoma and leukemia virus integrase suggests an alternate dimeric assembly. PMID:21857987
Evolutionary versatility of eukaryotic protein domains revealed by their bigram networks. PMID:21849086
A novel method to compare protein structures using local descriptors. PMID:21849047
Computational simulations to predict creatine kinase-associated factors: protein-protein interaction studies of brain and muscle types of creatine kinases. PMID:21826261
The Proteome Folding Project: proteome-scale prediction of structure and function. PMID:21824995
The Vein Patterning 1 (VEP1) gene family laterally spread through an ecological network. PMID:21818306
Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database. PMID:21801404
Fast side chain replacement in proteins using a coarse-grained approach for evaluating the effects of mutation during evolution. PMID:21800121
Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling. PMID:21791532
Small cofactors may assist protein emergence from RNA world: clues from RNA-protein complexes. PMID:21789260
Determination of protein fold class from Raman or Raman optical activity spectra using random forests. PMID:21766384
The significance of the ProtDeform score for structure prediction and alignment. PMID:21738592
Maps of protein structure space reveal a fundamental relationship between protein structure and function. PMID:21737750
CREST--a large and diverse superfamily of putative transmembrane hydrolases. PMID:21733186
Exploring the limits of fold discrimination by structural alignment: a large scale benchmark using decoys of known fold. PMID:21704264
Predicting protein folds with fold-specific PSSM libraries. PMID:21698189
Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs. PMID:21689388
The role of protein conformational fluctuations in allostery, function, and evolution. PMID:21684672
Structural principles within the human-virus protein-protein interaction network. PMID:21680884
Evolution: On a bender--BARs, ESCRTs, COPs, and finally getting your coat. PMID:21670211
Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates. PMID:21666270
Xwalk: computing and visualizing distances in cross-linking experiments. PMID:21666267
SA-Mot: a web server for the identification of motifs of interest extracted from protein loops. PMID:21665924
Water-mediated ionic interactions in protein structures. PMID:21654080
Relative solvent accessible surface area predicts protein conformational changes upon binding. PMID:21645856
Using linear algebra for protein structural comparison and classification. PMID:21637532
StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase. PMID:21635786
A network of SCOP hidden Markov models and its analysis. PMID:21635719
Structure of the three N-terminal immunoglobulin domains of the highly immunogenic outer capsid protein from a T4-like bacteriophage. PMID:21632759
An Algebro-topological description of protein domain structure. PMID:21629687
Structural insights on two hypothetical secretion chaperones from Xanthomonas axonopodis pv. citri. PMID:21626158
Absence of repellents in Ustilago maydis induces genes encoding small secreted proteins. PMID:21626092
Phosfinder: a web server for the identification of phosphate-binding sites on protein structures. PMID:21622655
Fractal symmetry of protein interior: what have we learned? PMID:21614471
The proteomic complexity and rise of the primordial ancestor of diversified life. PMID:21612591
Mapping the distribution of packing topologies within protein interiors shows predominant preference for specific packing motifs. PMID:21605466
CLICK--topology-independent comparison of biomolecular 3D structures. PMID:21602266
Biological insights from topology independent comparison of protein 3D structures. PMID:21596786
iPBA: a tool for protein structure comparison using sequence alignment strategies. PMID:21586582
Expression and β-glucan binding properties of Scots pine (Pinus sylvestris L.) antimicrobial protein (Sp-AMP). PMID:21584858
The N-terminal nucleophile serine of cephalosporin acylase executes the second autoproteolytic cleavage and acylpeptide hydrolysis. PMID:21576250
MetalDetector v2.0: predicting the geometry of metal binding sites from protein sequence. PMID:21576237
Certain heptapeptide and large sequences representing an entire helix, strand or coil conformation in proteins are associated as chameleon sequences. PMID:21569793
Virtual screening for potential inhibitors of homology modeled Leptospira interrogans MurD ligase. PMID:21566738
A bioinformatics classifier and database for heme-copper oxygen reductases. PMID:21559461
A library of protein surface patches discriminates between native structures and decoys generated by structure prediction servers. PMID:21542935
ModEnzA: Accurate Identification of Metabolic Enzymes Using Function Specific Profile HMMs with Optimised Discrimination Threshold and Modified Emission Probabilities. PMID:21541071
A topological framework for the computation of the HOMFLY polynomial and its application to proteins. PMID:21533239
A collaborative filtering approach for protein-protein docking scoring functions. PMID:21526112
Toward mechanistic classification of enzyme functions. PMID:21489855
Remote thioredoxin recognition using evolutionary conservation and structural dynamics. PMID:21481770
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. PMID:21472436
Touring protein space with Matt. PMID:21464511
Evaluating the solution from MrBUMP and BALBES. PMID:21460449
Improvement of molecular-replacement models with Sculptor. PMID:21460448
A protein domain co-occurrence network approach for predicting protein function and inferring species phylogeny. PMID:21455299
A systems biology approach for the investigation of the heparin/heparan sulfate interactome. PMID:21454685
A new approach to assess and predict the functional roles of proteins across all known structures. PMID:21445639
Identification of local conformational similarity in structurally variable regions of homologous proteins using protein blocks. PMID:21445259
HMMerThread: detecting remote, functional conserved domains in entire genomes by combining relaxed sequence-database searches with fold recognition. PMID:21423752
TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery. PMID:21408081
The regulatory subunit of PKA-I remains partially structured and undergoes β-aggregation upon thermal denaturation. PMID:21394209
Crystal structure of an integron gene cassette-associated protein from Vibrio cholerae identifies a cationic drug-binding module. PMID:21390267
Structural analysis of heme proteins: implications for design and prediction. PMID:21371326
Meet me halfway: when genomics meets structural bioinformatics. PMID:21350909
Normal modes of prion proteins: from native to infectious particle. PMID:21338080
Towards the prediction of protein interaction partners using physical docking. PMID:21326236
Bacterial protein structures reveal phylum dependent divergence. PMID:21315656
A mathematical framework for protein structure comparison. PMID:21304929
Detecting remote evolutionary relationships among proteins by large-scale semantic embedding. PMID:21298082
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank. PMID:21293729
A quality metric for homology modeling: the H-factor. PMID:21291572
Protein domain assignment from the recurrence of locally similar structures. PMID:21287617
Predicting protein flexibility through the prediction of local structures. PMID:21287616
DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning. PMID:21284866
Plasmodium vivax tryptophan-rich antigen PvTRAg33.5 contains alpha helical structure and multidomain architecture. PMID:21283717
The Dynameomics rotamer library: amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water. PMID:21280126
Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase. PMID:21278708
Identification of critical residues of the mycobacterial dephosphocoenzyme a kinase by site-directed mutagenesis. PMID:21264299
Poly-3-hydroxyalkanoate synthases from Pseudomonas putida U: substrate specificity and ultrastructural studies. PMID:21261834
Ara h 2: crystal structure and IgE binding distinguish two subpopulations of peanut allergic patients by epitope diversity. PMID:21255036
Crystal structure of a bacterial phosphoglucomutase, an enzyme involved in the virulence of multiple human pathogens. PMID:21246636
Gcn1 and actin binding to Yih1: implications for activation of the eIF2 kinase GCN2. PMID:21239490
Protein structure databases. PMID:21225378
1,000 structures and more from the MCSG. PMID:21219649
Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets. PMID:21183467
The combined effects of amino acid substitutions and indels on the evolution of structure within protein families. PMID:21179197
Cholera- and anthrax-like toxins are among several new ADP-ribosyltransferases. PMID:21170356
Some remarks on protein attribute prediction and pseudo amino acid composition. PMID:21168420
Symmetric key structural residues in symmetric proteins with beta-trefoil fold. PMID:21152439
Evolutionary innovations and the organization of protein functions in genotype space. PMID:21152394
Amino acid patterns around disulfide bonds. PMID:21151463
Structural space of protein-protein interfaces is degenerate, close to complete, and highly connected. PMID:21149688
iWRAP: An interface threading approach with application to prediction of cancer-related protein-protein interactions. PMID:21130772
Protein structure determination by exhaustive search of Protein Data Bank derived databases. PMID:21098306
Exploring the factors determining the dynamics of different protein folds. PMID:21086444
Prediction of a new class of RNA recognition motif. PMID:21082207
Proteome evolution and the metabolic origins of translation and cellular life. PMID:21082171
A data-mining approach for multiple structural alignment of proteins. PMID:21079664
A series of PDB related databases for everyday needs. PMID:21071423
The LabelHash algorithm for substructure matching. PMID:21070651
Generation of a consensus protein domain dictionary. PMID:21068000
ASD: a comprehensive database of allosteric proteins and modulators. PMID:21051350
Protein folds and protein folding. PMID:21051320
Characterizing the regularity of tetrahedral packing motifs in protein tertiary structure. PMID:21047817
Correlation to protein conformation of Wide-angle X-ray Scatter parameters. PMID:21046443
Structural analysis of Bacillus pumilus phenolic acid decarboxylase, a lipocalin-fold enzyme. PMID:21045284
ThYme: a database for thioester-active enzymes. PMID:21045059
X-ray structure and site-directed mutagenesis analysis of the Escherichia coli colicin M immunity protein. PMID:21037007
The protein common interface database (ProtCID)--a comprehensive database of interactions of homologous proteins in multiple crystal forms. PMID:21036862
Crystal structure of HugZ, a novel heme oxygenase from Helicobacter pylori. PMID:21030596
Clustering tendency in the protein fold space. PMID:20975898
Human glycolipid transfer protein gene (GLTP) expression is regulated by Sp1 and Sp3: involvement of the bioactive sphingolipid ceramide. PMID:20974858
Phosphate binding sites identification in protein structures. PMID:20974634
BriX: a database of protein building blocks for structural analysis, modeling and design. PMID:20972210
Identification of new homologs of PD-(D/E)XK nucleases by support vector machines trained on data derived from profile-profile alignments. PMID:20961958
Statistical analysis and molecular dynamics simulations of ambivalent α-helices. PMID:20955581
Characterization and comparison of two binding sites on obscurin for small ankyrin 1. PMID:20949908
Structure of a tryptophanyl-tRNA synthetase containing an iron-sulfur cluster. PMID:20944229
Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15. PMID:20944217
Structural classification of proteins and structural genomics: new insights into protein folding and evolution. PMID:20944210
TOPSAN: use of a collaborative environment for annotating, analyzing and disseminating data on JCSG and PSI structures. PMID:20944203
MEDELLER: homology-based coordinate generation for membrane proteins. PMID:20926421
Consistent picture of the reversible thermal unfolding of hen egg-white lysozyme from experiment and molecular dynamics. PMID:20923660
A global optimization algorithm for protein surface alignment. PMID:20920230
Position-specific propensities of amino acids in the β-strand. PMID:20920153
Evolutionary origin of a secondary structure: π-helices as cryptic but widespread insertional variations of α-helices that enhance protein functionality. PMID:20888342
Structural basis for the autoprocessing of zinc metalloproteases in the thermolysin family. PMID:20876133
Training a scoring function for the alignment of small molecules. PMID:20831240
Vorescore--fold recognition improved by rescoring of protein structure models. PMID:20823310
Protein-protein docking benchmark version 4.0. PMID:20806234
Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains. PMID:20799350
Characterization of Prochlorococcus clades from iron-depleted oceanic regions. PMID:20733077
Conformational optimization with natural degrees of freedom: a novel stochastic chain closure algorithm. PMID:20726792
TOPSAN: a collaborative annotation environment for structural genomics. PMID:20716366
Superpose3D: a local structural comparison program that allows for user-defined structure representations. PMID:20700534
Crystal structures of Phd-Doc, HigA, and YeeU establish multiple evolutionary links between microbial growth-regulating toxin-antitoxin systems. PMID:20696400
More than 1,001 problems with protein domain databases: transmembrane regions, signal peptides and the issue of sequence homology. PMID:20686689
Discovery of a new human polyomavirus associated with trichodysplasia spinulosa in an immunocompromized patient. PMID:20686659
DMDM: domain mapping of disease mutations. PMID:20685956
PROCARB: A Database of Known and Modelled Carbohydrate-Binding Protein Structures with Sequence-Based Prediction Tools. PMID:20671979
Protein subunit interfaces: A statistical analysis of hot spots in Sm proteins. PMID:20652820
Recognizing protein substructure similarity using segmental threading. PMID:20637422
iAlign: a method for the structural comparison of protein-protein interfaces. PMID:20624782
PDBWiki: added value through community annotation of the Protein Data Bank. PMID:20624717
Fine grained sampling of residue characteristics using molecular dynamics simulation. PMID:20621565
Automatic structure classification of small proteins using random forest. PMID:20594334
2010 ISCB Overton Prize Awarded to Steven E. Brenner. PMID:20585610
Beauty is in the eye of the beholder: proteins can recognize binding sites of homologous proteins in more than one way. PMID:20585553
The bridge-region of the Ku superfamily is an atypical zinc ribbon domain. PMID:20580930
What lessons can be learned from studying the folding of homologous proteins? PMID:20570731
Homology of SMP domains to the TULIP superfamily of lipid-binding proteins provides a structural basis for lipid exchange between ER and mitochondria. PMID:20554689
Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease. PMID:20551136
Quantifying the relationship between sequence and three-dimensional structure conservation in RNA. PMID:20550657
Spectroscopic and mechanistic investigations of dehaloperoxidase B from Amphitrite ornata. PMID:20545299
The C-terminal alpha-alpha superhelix of Pat is required for mRNA decapping in metazoa. PMID:20543818
A highly accurate statistical approach for the prediction of transmembrane beta-barrels. PMID:20538726
ProteinDBS v2.0: a web server for global and local protein structure search. PMID:20538653
Synonymous codon usage influences the local protein structure observed. PMID:20530529
Low-homology protein threading. PMID:20529920
dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment. PMID:20529369
Ontologies in quantitative biology: a basis for comparison, integration, and discovery. PMID:20520843
Retrospective analyses of the bottleneck in purification of eukaryotic proteins from Escherichia coli as affected by molecular weight, cysteine content and isoelectric point. PMID:20510014
Crystal structure of exotype alginate lyase Atu3025 from Agrobacterium tumefaciens. PMID:20507980
Conserved residue clusters at protein-protein interfaces and their use in binding site identification. PMID:20507585
Optimal contact definition for reconstruction of contact maps. PMID:20507547
How sequence directs bending in tropomyosin and other two-stranded alpha-helical coiled coils. PMID:20506487
Thioesterases: a new perspective based on their primary and tertiary structures. PMID:20506386
History of biological metal utilization inferred through phylogenomic analysis of protein structures. PMID:20498051
The Protein-DNA Interface database. PMID:20482798
Identification of a hypothetical protein from Podospora anserina as a nitroalkane oxidase. PMID:20481475
Diversity of function-related conformational changes in proteins: coordinate uncertainty, fragment rigidity, and stability. PMID:20469886
GIS: a comprehensive source for protein structure similarities. PMID:20460464
Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction. PMID:20459833
MTRAP: pairwise sequence alignment algorithm by a new measure based on transition probability between two consecutive pairs of residues. PMID:20459682
Distance-dependent statistical potentials for discriminating thermophilic and mesophilic proteins. PMID:20451495
ALADYN: a web server for aligning proteins by matching their large-scale motion. PMID:20444876
Structure, evolutionary conservation, and conformational dynamics of Homo sapiens fascin-1, an F-actin crosslinking protein. PMID:20434460
PoGO: Prediction of Gene Ontology terms for fungal proteins. PMID:20429880
Structural characteristics of novel protein folds. PMID:20421995
HangOut: generating clean PSI-BLAST profiles for domains with long insertions. PMID:20413635
PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences. PMID:20413579
Linear predictive coding representation of correlated mutation for protein sequence alignment. PMID:20406500
The domain structure of talin: residues 1815-1973 form a five-helix bundle containing a cryptic vinculin-binding site. PMID:20399778
Dynameomics: a comprehensive database of protein dynamics. PMID:20399180
How does the reductase help to regulate the catalytic cycle of cytochrome P450 3A4 using the conserved water channel? PMID:20387782
MrGrid: a portable grid based molecular replacement pipeline. PMID:20386612
MUSTANG-MR structural sieving server: applications in protein structural analysis and crystallography. PMID:20386610
Systematic search for putative new domain families in Mycoplasma gallisepticum genome. PMID:20384986
The evolution and functional repertoire of translation proteins following the origin of life. PMID:20377891
Alignment-free local structural search by writhe decomposition. PMID:20371498
Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data. PMID:20369061
A Stevedore's protein knot. PMID:20369018
The CATH database. PMID:20368142
Annular tautomerism: experimental observations and quantum mechanics calculations. PMID:20364360
Investigating homology between proteins using energetic profiles. PMID:20361049
A systematic survey of in vivo obligate chaperonin-dependent substrates. PMID:20360681
Structural analysis of Thermus thermophilus HB27 mannosyl-3-phosphoglycerate synthase provides evidence for a second catalytic metal ion and new insight into the retaining mechanism of glycosyltransferases. PMID:20356840
The ancient history of the structure of ribonuclease P and the early origins of Archaea. PMID:20334683
Origins of specificity in protein-DNA recognition. PMID:20334529
Physicochemical property distributions for accurate and rapid pairwise protein homology detection. PMID:20302613
Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function. PMID:20300652
A novel tool for classification of epidemiological data of vector-borne diseases. PMID:20300415
SeSAW: balancing sequence and structural information in protein functional mapping. PMID:20299324
New statistical potential for quality assessment of protein models and a survey of energy functions. PMID:20226048
Contact prediction for beta and alpha-beta proteins using integer linear optimization and its impact on the first principles 3D structure prediction method ASTRO-FOLD. PMID:20225257
SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale. PMID:20214776
Predicting highly-connected hubs in protein interaction networks by QSAR and biological data descriptors. PMID:20198194
Helix-sheet packing in proteins. PMID:20186972
Photox, a novel actin-targeting mono-ADP-ribosyltransferase from Photorhabdus luminescens. PMID:20181945
Structural and functional restraints on the occurrence of single amino acid variations in human proteins. PMID:20169194
Structural analysis and functional implications of the negative mTORC1 regulator REDD1. PMID:20166753
Structural determination and tryptophan fluorescence of heterokaryon incompatibility C2 protein (HET-C2), a fungal glycolipid transfer protein (GLTP), provide novel insights into glycolipid specificity and membrane interaction by the GLTP fold. PMID:20164530
How significant is a protein structure similarity with TM-score = 0.5? PMID:20164152
Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins. PMID:20162627
Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison. PMID:20158924
The overlap of small molecule and protein binding sites within families of protein structures. PMID:20140189
FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately. PMID:20133727
Six Rossmannoid folds, including the Class I aminoacyl-tRNA synthetases, share a partial core with the anti-codon-binding domain of a Class II aminoacyl-tRNA synthetase. PMID:20130031
Prediction of protein structural classes for low-homology sequences based on predicted secondary structure. PMID:20122246
A fast indexing approach for protein structure comparison. PMID:20122220
Efficient protein alignment algorithm for protein search. PMID:20122207
HORI: a web server to compute Higher Order Residue Interactions in protein structures. PMID:20122196
Classification of protein sequences by means of irredundant patterns. PMID:20122187
BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server. PMID:20100327
Sequence and structural analysis of the chitinase insertion domain reveals two conserved motifs involved in chitin-binding. PMID:20084296
Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be. PMID:20081223
Active site prediction using evolutionary and structural information. PMID:20080507
Protein structure prediction enhanced with evolutionary diversity: SPEED. PMID:20066664
Conformational transitions upon ligand binding: holo-structure prediction from apo conformations. PMID:20066034
Homologous over-extension: a challenge for iterative similarity searches. PMID:20064877
DsrR, a novel IscA-like protein lacking iron- and Fe-S-binding functions, involved in the regulation of sulfur oxidation in Allochromatium vinosum. PMID:20061482
Comparison of human solute carriers. PMID:20052679
Comparative genomic and phylogenetic analyses reveal the evolution of the core two-component signal transduction systems in enterobacteria. PMID:20049425
Quality measures for protein alignment benchmarks. PMID:20047958
Three dimensional structure of the MqsR:MqsA complex: a novel TA pair comprised of a toxin homologous to RelE and an antitoxin with unique properties. PMID:20041169
Mapping of ligand-binding cavities in proteins. PMID:20034113
svmPRAT: SVM-based protein residue annotation toolkit. PMID:20028521
An automated procedure for detecting protein folds from sub-nanometer resolution electron density. PMID:20026407
Prediction of backbone dihedral angles and protein secondary structure using support vector machines. PMID:20025785
Short paths in protein structure space originate in graph structure. PMID:20018710
Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution. PMID:20018669
De novo backbone scaffolds for protein design. PMID:20017215
DescFold: a web server for protein fold recognition. PMID:20003426
TIM-Finder: a new method for identifying TIM-barrel proteins. PMID:20003393
Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences. PMID:20003388
Defining an essence of structure determining residue contacts in proteins. PMID:19997489
Dynameomics: a consensus view of the protein unfolding/folding transition state ensemble across a diverse set of protein folds. PMID:19948125
Disulfide conformation and design at helix N-termini. PMID:19938155
A galaxy of folds. PMID:19937658
The structure of the mammalian RNase H2 complex provides insight into RNA.NA hybrid processing to prevent immune dysfunction. PMID:19923215
Structure of a eukaryotic nonribosomal peptide synthetase adenylation domain that activates a large hydroxamate amino acid in siderophore biosynthesis. PMID:19923209
SitesIdentify: a protein functional site prediction tool. PMID:19922660
Analysis of HSP90-related folds with MED-SuMo classification approach. PMID:19920922
Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain. PMID:19913036
A threading-based method for the prediction of DNA-binding proteins with application to the human genome. PMID:19911048
Computational exploration of the network of sequence flow between protein structures. PMID:19899165
The PHCCEx domain of Tiam1/2 is a novel protein- and membrane-binding module. PMID:19893486
Catalytic mechanism of bleomycin N-acetyltransferase proposed on the basis of its crystal structure. PMID:19889644
fPOP: footprinting functional pockets of proteins by comparative spatial patterns. PMID:19880384
(PS)2-v2: template-based protein structure prediction server. PMID:19878598
The role of UPF0157 in the folding of M. tuberculosis dephosphocoenzyme A kinase and the regulation of the latter by CTP. PMID:19876400
Mechanical strength of 17,134 model proteins and cysteine slipknots. PMID:19876372
The role of DNA shape in protein-DNA recognition. PMID:19865164
Finding of residues crucial for supersecondary structure formation. PMID:19855006
A structure filter for the Eukaryotic Linear Motif Resource. PMID:19852836
Reconciling theories of chaperonin accelerated folding with experimental evidence. PMID:19851829
Amino acid and structural variability of Yersinia pestis LcrV protein. PMID:19835996
Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human. PMID:19833706
Deciphering the structural basis that guides the oxidative folding of leech-derived tryptase inhibitor. PMID:19820233
Utility of computational methods to identify the apoptosis machinery in unicellular eukaryotes. PMID:19812769
Characterization of non-trivial neighborhood fold constraints from protein sequences using generalized topohydrophobicity. PMID:19812765
Predictive chromatin signatures in the mammalian genome. PMID:19808796
Fast screening of protein surfaces using geometric invariant fingerprints. PMID:19805347
Betaalpha-hairpin clamps brace betaalphabeta modules and can make substantive contributions to the stability of TIM barrel proteins. PMID:19787060
Highly sensitive detection of individual HEAT and ARM repeats with HHpred and COACH. PMID:19777061
End-to-end and end-to-middle interhelical interactions: new classes of interacting helix pairs in protein structures. PMID:19770500
The crystal structure of the AF2331 protein from Archaeoglobus fulgidus DSM 4304 forms an unusual interdigitated dimer with a new type of alpha + beta fold. PMID:19768810
3D-footprint: a database for the structural analysis of protein-DNA complexes. PMID:19767616
Exploring protein structural dissimilarity to facilitate structure classification. PMID:19765314
Three-dimensional structural view of the central metabolic network of Thermotoga maritima. PMID:19762644
Prodepth: predict residue depth by support vector regression approach from protein sequences only. PMID:19759917
Crystal structure of a mucus-binding protein repeat reveals an unexpected functional immunoglobulin binding activity. PMID:19758995
Structural and functional constraints in the evolution of protein families. PMID:19756040
Comparison of structure-based and threading-based approaches to protein functional annotation. PMID:19731377
Theoretical characterization of substrate access/exit channels in the human cytochrome P450 3A4 enzyme: involvement of phenylalanine residues in the gating mechanism. PMID:19728720
Transcriptome and protein domain analyses in Aplysia nervous system with evolutionary implications. PMID:19721878
The crystal structure of the Escherichia coli autoinducer-2 processing protein LsrF. PMID:19714241
FLORA: a novel method to predict protein function from structure in diverse superfamilies. PMID:19714201
Computation of conformational coupling in allosteric proteins. PMID:19714199
Structural analysis of polarizing indels: an emerging consensus on the root of the tree of life. PMID:19706177
The CATH hierarchy revisited-structural divergence in domain superfamilies and the continuity of fold space. PMID:19679085
Comprehensive computational analysis of Hmd enzymes and paralogs in methanogenic Archaea. PMID:19671178
Alteration of oligomeric state and domain architecture is essential for functional transformation between transferase and hydrolase with the same scaffold. PMID:19670211
Oxidation of amines by flavoproteins. PMID:19651103
Coupling between properties of the protein shape and the rate of protein folding. PMID:19649298
The evolutionary history of the structure of 5S ribosomal RNA. PMID:19639237
Harvesting candidate genes responsible for serious adverse drug reactions from a chemical-protein interactome. PMID:19629158
Structure of signal-regulatory protein alpha: a link to antigen receptor evolution. PMID:19628875
Enhancement of beta-sheet assembly by cooperative hydrogen bonds potential. PMID:19628506
Accuracy analysis of multiple structure alignments. PMID:19621383
Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS). PMID:19620974
Understanding structural features of microbial lipases--an overview. PMID:19609386
PSPP: a protein structure prediction pipeline for computing clusters. PMID:19606223
Target domain definition and classification in CASP8. PMID:19603487
Conformational changes in redox pairs of protein structures. PMID:19598234
A comprehensive bioinformatics analysis of the Nudix superfamily in Arabidopsis thaliana. PMID:19590748
Analyses on hydrophobicity and attractiveness of all-atom distance-dependent potentials. PMID:19588493
Alignment of multiple protein structures based on sequence and structure features. PMID:19587024
Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation. PMID:19578405
Alpha helical crossovers favor right-handed supersecondary structures by kinetic trapping: the phone cord effect in protein folding. PMID:19569186
Relative stabilities of conserved and non-conserved structures in the OB-fold superfamily. PMID:19564956
Remote homology between Munc13 MUN domain and vesicle tethering complexes. PMID:19563813
Ab initio and homology based prediction of protein domains by recursive neural networks. PMID:19558651
Optimized null model for protein structure networks. PMID:19557139
Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: II. Case studies and applications. PMID:19548090
Nature of the protein universe. PMID:19541617
The R46Q, R131Q and R154H polymorphs of human DNA glycosylase/beta-lyase hOgg1 severely distort the active site and DNA recognition site but do not cause unfolding. PMID:19537786
A chemogenomics view on protein-ligand spaces. PMID:19534738
Effective knowledge-based potentials. PMID:19530247
Ranaspumin-2: structure and function of a surfactant protein from the foam nests of a tropical frog. PMID:19527658
Structural motifs recurring in different folds recognize the same ligand fragments. PMID:19527512
Characterization of the kringle fold and identification of a ubiquitous new class of disulfide rotamers. PMID:19524679
PSI-2: structural genomics to cover protein domain family space. PMID:19523904
FINDSITE: a threading-based approach to ligand homology modeling. PMID:19503616
Using genome-wide measurements for computational prediction of SH2-peptide interactions. PMID:19502496
Cavities in protein-DNA and protein-RNA interfaces. PMID:19494181
Reconstruction and stability of secondary structure elements in the context of protein structure prediction. PMID:19486664
Origin of saxitoxin biosynthetic genes in cyanobacteria. PMID:19484122
Structure-based phylogeny as a diagnostic for functional characterization of proteins with a cupin fold. PMID:19478949
Evolutionary constraints on structural similarity in orthologs and paralogs. PMID:19472362
CORAL: aligning conserved core regions across domain families. PMID:19470584
d-Omix: a mixer of generic protein domain analysis tools. PMID:19465389
COPS--a novel workbench for explorations in fold space. PMID:19465386
The SALAMI protein structure search server. PMID:19465380
Universal partitioning of the hierarchical fold network of 50-residue segments in proteins. PMID:19454039
Improving protein structure similarity searches using domain boundaries based on conserved sequence information. PMID:19454035
Tableau-based protein substructure search using quadratic programming. PMID:19450287
MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming. PMID:19443443
Studying the folding of multidomain proteins. PMID:19436439
The Rho GTPase inactivation domain in Vibrio cholerae MARTX toxin has a circularly permuted papain-like thiol protease fold. PMID:19434753
HHomp--prediction and classification of outer membrane proteins. PMID:19429691
Vaccinia virus G8R protein: a structural ortholog of proliferating cell nuclear antigen (PCNA). PMID:19421403
ProSMoS server: a pattern-based search using interaction matrix representation of protein structures. PMID:19420061
HorA web server to infer homology between proteins using sequence and structural similarity. PMID:19417074
RASMOT-3D PRO: a 3D motif search webserver. PMID:19417073
Flexible structural protein alignment by a sequence of local transformations. PMID:19417057
Substrate specificity of streptococcal unsaturated glucuronyl hydrolases for sulfated glycosaminoglycan. PMID:19416976
Improving classification in protein structure databases using text mining. PMID:19416501
Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs. PMID:19393049
Augmented training of hidden Markov models to recognize remote homologs via simulated evolution. PMID:19389731
Active site conformational changes of prostasin provide a new mechanism of protease regulation by divalent cations. PMID:19388054
The crystal structures of Chikungunya and Venezuelan equine encephalitis virus nsP3 macro domains define a conserved adenosine binding pocket. PMID:19386706
Island method for estimating the statistical significance of profile-profile alignment scores. PMID:19379500
Structure and mechanism of a eukaryotic FMN adenylyltransferase. PMID:19375431
Structural analysis of a monomeric form of the twin-arginine leader peptide binding chaperone Escherichia coli DmsD. PMID:19361518
Structural and motional contributions of the Bacillus subtilis ClpC N-domain to adaptor protein interactions. PMID:19361434
Molecular dynamism of Fe-S cluster biosynthesis implicated by the structure of the SufC(2)-SufD(2) complex. PMID:19361433
PROCAIN: protein profile comparison with assisting information. PMID:19357092
A database of domain definitions for proteins with complex interdomain geometry. PMID:19352501
Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment. PMID:19351620
Stochastic reconstruction of protein structures from effective connectivity profiles. PMID:19351427
Length variations amongst protein domain superfamilies and consequences on structure and function. PMID:19333395
Building and assessing atomic models of proteins from structural templates: learning and benchmarks. PMID:19326457
Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures. PMID:19325884
FINDSITE: a combined evolution/structure-based approach to protein function prediction. PMID:19324930
Structure and heme binding properties of Escherichia coli O157:H7 ChuX. PMID:19319934
Energetic profiling of protein folds. PMID:19289211
TFCat: the curated catalog of mouse and human transcription factors. PMID:19284633
Structural conservation of a short, functional, peptide-sequence motif. PMID:19273121
Glycolipid acquisition by human glycolipid transfer protein dramatically alters intrinsic tryptophan fluorescence: insights into glycolipid binding affinity. PMID:19270338
Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins. PMID:19251648
Protein structure prediction on the Web: a case study using the Phyre server. PMID:19247286
A new prediction strategy for long local protein structures using an original description. PMID:19241475
Crystal structure of YfeU protein from Haemophilus influenzae: a predicted etherase involved in peptidoglycan recycling. PMID:19234762
Sequence context-specific profiles for homology searching. PMID:19234132
Identification of DNA-binding proteins using structural, electrostatic and evolutionary features. PMID:19233205
Are protein domains modules of lateral genetic transfer? PMID:19229333
Protein function annotation by homology-based inference. PMID:19226439
The Kir channel immunoglobulin domain is essential for Kir1.1 (ROMK) thermodynamic stability, trafficking and gating. PMID:19221509
X-Ray crystallographic and mutational studies of fluoroacetate dehalogenase from Burkholderia sp. strain FA1. PMID:19218394
Structural basis of murein peptide specificity of a gamma-D-glutamyl-l-diamino acid endopeptidase. PMID:19217401
A new computational model to study mass inhomogeneity and hydrophobicity inhomogeneity in proteins. PMID:19214496
Electrostatic and functional analysis of the seven-bladed WD beta-propellers. PMID:19204818
Structural genomics is the largest contributor of novel structural leverage. PMID:19194785
Structure of the thioredoxin-fold domain of human phosducin-like protein 2. PMID:19193988
Structural genomics reveals EVE as a new ASCH/PUA-related domain. PMID:19191354
Universal features in the genome-level evolution of protein domains. PMID:19183449
Protein domain organisation: adding order. PMID:19178743
Generalized ensemble methods for de novo structure prediction. PMID:19171891
VASCo: computation and visualization of annotated protein surface contacts. PMID:19166624
Predicting protein function and binding profile via matching of local evolutionary and geometric surface patterns. PMID:19154742
Domain mobility in proteins: functional and evolutionary implications. PMID:19151098
Fre Is the Major Flavin Reductase Supporting Bioluminescence from Vibrio harveyi Luciferase in Escherichia coli. PMID:19139094
Structural model of the Rev regulatory protein from equine infectious anemia virus. PMID:19137065
Structural alphabets for protein structure classification: a comparison study. PMID:19135454
Characterization of the yellow fever mosquito sterol carrier protein-2 like 3 gene and ligand-bound protein structure. PMID:19130179
Mesothelin, Stereocilin, and Otoancorin are predicted to have superhelical structures with ARM-type repeats. PMID:19128473
Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families. PMID:19111067
The meaning of alignment: lessons from structural diversity. PMID:19105835
NMR and X-RAY structures of human E2-like ubiquitin-fold modifier conjugating enzyme 1 (UFC1) reveal structural and functional conservation in the metazoan UFM1-UBA5-UFC1 ubiquination pathway. PMID:19101823
PocketMatch: a new algorithm to compare binding sites in protein structures. PMID:19091072
PSI-BLAST pseudocounts and the minimum description length principle. PMID:19088134
Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score. PMID:19077267
Improved prediction of malaria degradomes by supervised learning with SVM and profile kernel. PMID:19057851
FIEFDom: a transparent domain boundary recognition system using a fuzzy mean operator. PMID:19056827
Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues. PMID:19056820
The 1.6 A crystal structure of Mycobacterium smegmatis MshC: the penultimate enzyme in the mycothiol biosynthetic pathway. PMID:19053270
Functional proteomic and structural insights into molecular recognition in the nitrilase family enzymes. PMID:19053248
Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold. PMID:19052085
Characterization of serine proteinase expression in Agaricus bisporus and Coprinopsis cinerea by using green fluorescent protein and the A. bisporus SPR1 promoter. PMID:19047386
Structural studies of shikimate dehydrogenase from Bacillus anthracis complexed with cofactor NADP. PMID:19043750
Local descriptors of protein structure: a systematic analysis of the sequence-structure relationship in proteins using short- and long-range interactions. PMID:19025980
Insights into the evolutionary origins of clostridial neurotoxins from analysis of the Clostridium botulinum strain A neurotoxin gene cluster. PMID:19014598
Protein subfamily assignment using the Conserved Domain Database. PMID:19014584
Towards predicting Ca2+-binding sites with different coordination numbers in proteins with atomic resolution. PMID:19003991
RANKPROP: a web server for protein remote homology detection. PMID:18990723
Protein segment finder: an online search engine for segment motifs in the PDB. PMID:18974183
NMR solution structure of the neurotrypsin Kringle domain. PMID:18956887
Prediction of protein structural classes using hybrid properties. PMID:18953662
RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases. PMID:18953028
2S Albumin Storage Proteins: What Makes them Food Allergens? PMID:18949071
ProSeg: a database of local structures of protein segments. PMID:18931918
Structure of a 6-pyruvoyltetrahydropterin synthase homolog from Streptomyces coelicolor. PMID:18931427
Structural assembly of two-domain proteins by rigid-body docking. PMID:18925951
Prediction of TF target sites based on atomistic models of protein-DNA complexes. PMID:18922190
CC+: a relational database of coiled-coil structures. PMID:18842638
CPDB: a database of circular permutation in proteins. PMID:18842637
KineticDB: a database of protein folding kinetics. PMID:18842631
Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution. PMID:18840284
A method for probabilistic mapping between protein structure and function taxonomies through cross training. PMID:18834528
Discarding functional residues from the substitution table improves predictions of active sites within three-dimensional structures. PMID:18833291
The interconversion of ACC deaminase and D-cysteine desulfhydrase by directed mutagenesis. PMID:18825405
Searching protein structure databases with DaliLite v.3. PMID:18818215
Combining classifiers for improved classification of proteins from sequence or structure. PMID:18808707
Amino acid composition and protein dimension. PMID:18780815
Towards accurate residue-residue hydrophobic contact prediction for alpha helical proteins via integer linear optimization. PMID:18767158
Similar modes of interaction enable Trailer Hitch and EDC3 to associate with DCP1 and Me31B in distinct protein complexes. PMID:18765641
Structural and functional studies indicate that Shigella VirA is not a protease and does not directly destabilize microtubules. PMID:18763811
TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model. PMID:18759993
Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli. PMID:18723842
Classifying RNA-binding proteins based on electrostatic properties. PMID:18716674
An enhanced partial order curve comparison algorithm and its application to analyzing protein folding trajectories. PMID:18710565
Protein-segment universe exhibiting transitions at intermediate segment length in conformational subspaces. PMID:18700043
Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family. PMID:18700034
Powerful fusion: PSI-BLAST and consensus sequences. PMID:18678588
Structural similarity of genetically interacting proteins. PMID:18671848
Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies. PMID:18670595
Predicting and validating protein interactions using network structure. PMID:18654616
Short strong hydrogen bonds in proteins: a case study of rhamnogalacturonan acetylesterase. PMID:18645234
MSDmotif: exploring protein sites and motifs. PMID:18637174
A beta alpha-barrel built by the combination of fragments from different folds. PMID:18632584
Flowering buds of globular proteins: transpiring simplicity of protein organization. PMID:18629251
The cadherin superfamily in Anopheles gambiae: a comparative study with Drosophila melanogaster. PMID:18629193
A computational strategy for protein function assignment which addresses the multidomain problem. PMID:18629055
Solution structure of the U2 snRNP protein Rds3p reveals a knotted zinc-finger motif. PMID:18621724
Comprehensive 3D-modeling of allergenic proteins and amino acid composition of potential conformational IgE epitopes. PMID:18621419
Architectures and functional coverage of protein-protein interfaces. PMID:18620705
Local alignment refinement using structural assessment. PMID:18612410
Statistical analysis of interface similarity in crystals of homologous proteins. PMID:18599072
Contextual specificity in peptide-mediated protein interactions. PMID:18596940
Statistical analysis of structural characteristics of protein Ca2+-binding sites. PMID:18594878
Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. PMID:18586742
The effectiveness of position- and composition-specific gap costs for protein similarity searches. PMID:18586708
Novel protein folds and their nonsequential structural analogs. PMID:18583523
Effects of surface-to-volume ratio of proteins on hydrophilic residues: decrease in occurrence and increase in buried fraction. PMID:18556475
PURE: a webserver for the prediction of domains in unassigned regions in proteins. PMID:18554415
Protein structural class prediction based on an improved statistical strategy. PMID:18541058
Evolutionary conservation of DNA-contact residues in DNA-binding domains. PMID:18541056
SP5: improving protein fold recognition by using torsion angle profiles and profile-based gap penalty model. PMID:18523556
Word correlation matrices for protein sequence analysis and remote homology detection. PMID:18522726
CUSP: an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations. PMID:18513436
Ribonuclease A homologues of the zebrafish: polymorphism, crystal structures of two representatives and their evolutionary implications. PMID:18508078
SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser. PMID:18503088
PROMALS3D web server for accurate multiple protein sequence and structure alignments. PMID:18503087
Domain Hierarchy and closed Loops (DHcL): a server for exploring hierarchy of protein domain structure. PMID:18502776
SARSA: a web tool for structural alignment of RNA using a structural alphabet. PMID:18502774
Signature genes as a phylogenomic tool. PMID:18492663
Protein-protein docking benchmark version 3.0. PMID:18491384
Reconstruction of protein backbones from the BriX collection of canonical protein fragments. PMID:18483555
Sequence similarity network reveals common ancestry of multidomain proteins. PMID:18475320
The role of DNA-binding specificity in the evolution of bacterial regulatory networks. PMID:18466918
The Jpred 3 secondary structure prediction server. PMID:18463136
Prediction of interacting single-stranded RNA bases by protein-binding patterns. PMID:18452949
SCPRED: accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences. PMID:18452616
Using multiple templates to improve quality of homology models in automated homology modeling. PMID:18441233
Structures, basins, and energies: a deconstruction of the Protein Coil Library. PMID:18434497
Constructing templates for protein structure prediction by simulation of protein folding pathways. PMID:18433063
Overview of protein structural and functional folds. PMID:18429251
Regulation of membrane proteins by dietary lipids: effects of cholesterol and docosahexaenoic acid acyl chain-containing phospholipids on rhodopsin stability and function. PMID:18424497
Bridging protein local structures and protein functions. PMID:18421562
Discriminative learning for protein conformation sampling. PMID:18412258
Golgi localization of glycosyltransferases requires a Vps74p oligomer. PMID:18410729
Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering. PMID:18402669
Nature of protein family signatures: insights from singular value analysis of position-specific scoring matrices. PMID:18398479
Rethinking proteasome evolution: two novel bacterial proteasomes. PMID:18389302
Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. PMID:18385384
Alignment of non-covalent interactions at protein-protein interfaces. PMID:18382693
Correspondences between low-energy modes in enzymes: dynamics-based alignment of enzymatic functional families. PMID:18369194
The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches. PMID:18369181
A simple and fast heuristic for protein structure comparison. PMID:18366735
Fibril growth kinetics reveal a region of beta2-microglobulin important for nucleation and elongation of aggregation. PMID:18342332
Tel2 mediates activation and localization of ATM/Tel1 kinase to a double-strand break. PMID:18334620
SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803. PMID:18315852
Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable data sets. PMID:18313074
A template-finding algorithm and a comprehensive benchmark for homology modeling of proteins. PMID:18300226
On the relation between the predicted secondary structure and the protein size. PMID:18299971
Homology and phylogeny and their automated inference. PMID:18288471
PROMALS3D: a tool for multiple protein sequence and structure alignments. PMID:18287115
Accurate statistical model of comparison between multiple sequence alignments. PMID:18285364
Anatomy of the E2 ligase fold: implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation. PMID:18276160
Protein structure fitting and refinement guided by cryo-EM density. PMID:18275820
Analysis of the human kinome using methods including fold recognition reveals two novel kinases. PMID:18270584
Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction. PMID:18267018
Protein databases on the internet. PMID:18265344
Human glycolipid transfer protein (GLTP) genes: organization, transcriptional status and evolution. PMID:18261224
MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information. PMID:18247410
Towards an automatic classification of protein structural domains based on structural similarity. PMID:18237410
Molecular modelling and comparative structural account of aspartyl beta-semialdehyde dehydrogenase of Mycobacterium tuberculosis (H37Rv). PMID:18236087
Fast dynamics perturbation analysis for prediction of protein functional sites. PMID:18234095
Functional site profiling and electrostatic analysis of cysteines modifiable to cysteine sulfenic acid. PMID:18227433
The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction. PMID:18221517
Discrimination of outer membrane proteins with improved performance. PMID:18218108
The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation. PMID:18197987
Matt: local flexibility aids protein multiple structure alignment. PMID:18193941
The animal in the genome: comparative genomics and evolution. PMID:18192189
Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. PMID:18190718
In silico chaperonin-like cycle helps folding of proteins for structure prediction. PMID:18178656
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. PMID:18165317
Background frequencies for residue variability estimates: BLOSUM revisited. PMID:18162129
LTHREADER: prediction of extracellular ligand-receptor interactions in cytokines using localized threading. PMID:18096641
The JCSG MR pipeline: optimized alignments, multiple models and parallel searches. PMID:18094477
BALBES: a molecular-replacement pipeline. PMID:18094476
MrBUMP: an automated pipeline for molecular replacement. PMID:18094475
Model preparation in MOLREP and examples of model improvement using X-ray data. PMID:18094465
Building an understanding of cystic fibrosis on the foundation of ABC transporter structures. PMID:18080175
DBD--taxonomically broad transcription factor predictions: new content and functionality. PMID:18073188
Domain architecture and biochemical characterization of vertebrate Mcm10. PMID:18065420
The yeast ribosome synthesis factor Emg1 is a novel member of the superfamily of alpha/beta knot fold methyltransferases. PMID:18063569
Identifying foldable regions in protein sequence from the hydrophobic signal. PMID:18056079
Probing protein fold space with a simplified model. PMID:18054792
Predicting and improving the protein sequence alignment quality by support vector regression. PMID:18053160
CATHEDRAL: a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures. PMID:18052539
Using likelihood-free inference to compare evolutionary dynamics of the protein networks of H. pylori and P. falciparum. PMID:18052538
The hypothetical protein Atu4866 from Agrobacterium tumefaciens adopts a streptavidin-like fold. PMID:18042676
STRALCP--structure alignment-based clustering of proteins. PMID:18039711
Crosstalk between the protein surface and hydrophobic core in a core-swapped fibronectin type III domain. PMID:18035373
Gene3D: comprehensive structural and functional annotation of genomes. PMID:18032434
Molecular crowding inhibits intramolecular breathing motions in proteins. PMID:18031757
A comprehensive analysis of non-sequential alignments between all protein structures. PMID:18005453
Insertions and the emergence of novel protein structure: a structure-based phylogenetic study of insertions. PMID:18005425
Data growth and its impact on the SCOP database: new developments. PMID:18000004
Modeling protein network evolution under genome duplication and domain shuffling. PMID:17999763
Determinants of protein function revealed by combinatorial entropy optimization. PMID:17976239
SABERTOOTH: protein structural alignment based on a vectorial structure representation. PMID:17974011
Novel hexamerization motif is discovered in a conserved cytoplasmic protein from Salmonella typhimurium. PMID:17968677
Host pathogen protein interactions predicted by comparative modeling. PMID:17965183
Application of amino acid occurrence for discriminating different folding types of globular proteins. PMID:17953741
Characterization of protein hubs by inferring interacting motifs from protein interactions. PMID:17941705
Side-chain protonation and mobility in the sarcoplasmic reticulum Ca2+-ATPase: implications for proton countertransport and Ca2+ release. PMID:17938423
Topology independent protein structural alignment. PMID:17937816
MegaMotifBase: a database of structural motifs in protein families and superfamilies. PMID:17933773
Development of a heme protein structure-electrochemical function database. PMID:17933771
Spatial chemical conservation of hot spot interactions in protein-protein complexes. PMID:17925020
A divergent Sm fold in EDC3 proteins mediates DCP1 binding and P-body targeting. PMID:17923697
Nitrosative stress treatment of E. coli targets distinct set of thiol-containing proteins. PMID:17919278
Analysis on sliding helices and strands in protein structural comparisons: a case study with protein kinases. PMID:17914234
DOMINE: a database of protein domain interactions. PMID:17913741
Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world. PMID:17908824
Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties. PMID:17888146
Functional insights from structures of coactivator-associated arginine methyltransferase 1 domains. PMID:17882262
Classification of protein folds. PMID:17873410
MALISAM: a database of structurally analogous motifs in proteins. PMID:17855399
Amino-acid interactions in psychrophiles, mesophiles, thermophiles, and hyperthermophiles: insights from the quasi-chemical approximation. PMID:17766385
Solution structure of the hypothetical protein TA0095 from Thermoplasma acidophilum: a novel superfamily with a two-layer sandwich architecture. PMID:17766377
Automatic generation of 3D motifs for classification of protein binding sites. PMID:17760982
Visualization software for molecular assemblies. PMID:17728125
Distribution patterns of small-molecule ligands in the protein universe and implications for origin of life and drug discovery. PMID:17727706
Spectrum of disease-causing mutations in protein secondary structures. PMID:17727703
Protein disulfide oxidoreductases and the evolution of thermophily: was the last common ancestor a heat-loving microbe? PMID:17726569
A comprehensive system for evaluation of remote sequence similarity detection. PMID:17725841
PROCOGNATE: a cognate ligand domain mapping for enzymes. PMID:17720712
The RAGNYA fold: a novel fold with multiple topological variants found in functionally diverse nucleic acid, nucleotide and peptide-binding proteins. PMID:17715145
Automated protein subfamily identification and classification. PMID:17708678
Multiple domain insertions and losses in the evolution of the Rab prenylation complex. PMID:17705859
Structural footprinting in protein structure comparison: the impact of structural fragments. PMID:17688700
Crystal structure of the Escherichia coli regulator of sigma70, Rsd, in complex with sigma70 domain 4. PMID:17681541
Partially folded states of staphylococcal nuclease highlight the conserved structural hierarchy of OB-fold proteins. PMID:17661445
Evolution of function in the "two dinucleotide binding domains" flavoproteins. PMID:17658942
Simulation study on the disordered state of an Alzheimer's beta amyloid peptide Abeta(12 36) in water consisting of random-structural, beta-structural, and helical clusters. PMID:17656579
Building native protein conformation from NMR backbone chemical shifts using Monte Carlo fragment assembly. PMID:17656574
Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment. PMID:17629909
Crystal structure of an acetyltransferase protein from Vibrio cholerae strain N16961. PMID:17623843
Hypothetical protein AF2241 from Archaeoglobus fulgidus adopts a cyclophilin-like fold. PMID:17610131
A topological algorithm for identification of structural domains of proteins. PMID:17608939
Small but versatile: the extraordinary functional and structural diversity of the beta-grasp fold. PMID:17605815
Beta barrel trans-membrane proteins: Enhanced prediction using a Bayesian approach. PMID:17597895
A predictor of membrane class: Discriminating alpha-helical and beta-barrel membrane proteins from non-membranous proteins. PMID:17597890
The network of sequence flow between protein structures. PMID:17596339
Evolutionary history and functional implications of protein domains and their combinations in eukaryotes. PMID:17588271
NMR structure of a KlbA intein precursor from Methanococcus jannaschii. PMID:17586768
Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches. PMID:17584917
Using structural motif descriptors for sequence-based binding site prediction. PMID:17570148
SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition. PMID:17570145
The 2006 automated function prediction meeting. PMID:17570143
Comprehensive analysis of co-occurring domain sets in yeast proteins. PMID:17562021
siteFiNDER|3D: a web-based tool for predicting the location of functional sites in proteins. PMID:17553829
Structure of a complex of human lactoferrin N-lobe with pneumococcal surface protein a provides insight into microbial defense mechanism. PMID:17543335
StrBioLib: a Java library for development of custom computational structural biology applications. PMID:17537750
Hinge Atlas: relating protein sequence to sites of structural flexibility. PMID:17519025
The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture. PMID:17517598
How accurate and statistically robust are catalytic site predictions based on closeness centrality? PMID:17498304
Structural and functional insights into Mimivirus ORFans. PMID:17490476
QSCOP-BLAST--fast retrieval of quantified structural information for protein sequences of unknown structure. PMID:17478501
In silico prediction of SARS protease inhibitors by virtual high throughput screening. PMID:17461975
DDOMAIN: Dividing structures into domains using a normalized domain-domain interaction profile. PMID:17456745
PROMALS web server for accurate multiple protein sequence alignments. PMID:17452345
Comparison of sequence-based and structure-based phylogenetic trees of homologous proteins: Inferences on protein evolution. PMID:17426382
"Pinning strategy": a novel approach for predicting the backbone structure in terms of protein blocks from sequence. PMID:17426380
BranchClust: a phylogenetic algorithm for selecting gene families. PMID:17425803
Protein homologous cores and loops: important clues to evolutionary relationships between structurally similar proteins. PMID:17425794
Identification of the FANCI protein, a monoubiquitinated FANCD2 paralog required for DNA repair. PMID:17412408
ASH structure alignment package: sensitivity and selectivity in domain classification. PMID:17407606
Improved residue contact prediction using support vector machines and a large feature set. PMID:17407573
Using reaction mechanism to measure enzyme similarity. PMID:17400244
HMM-ModE--improved classification using profile hidden Markov models by optimising the discrimination threshold and modifying emission probabilities with negative training sequences. PMID:17389042
Inherent chaperone-like activity of aspartic proteases reveals a distant evolutionary relation to double-psi barrel domains of AAA-ATPases. PMID:17384229
Positive and negative design in stability and thermal adaptation of natural proteins. PMID:17381236
The Arabidopsis thaliana AT PRP39-1 gene, encoding a tetratricopeptide repeat protein with similarity to the yeast pre-mRNA processing protein PRP39, affects flowering time. PMID:17380304
Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PMID:17373854
Topology of Type II REases revisited; structural classes and the common conserved core. PMID:17369272
Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments. PMID:17369271
The folding mechanics of a knotted protein. PMID:17368671
Growth of novel protein structural data. PMID:17360626
Near-native structure refinement using in vacuo energy minimization. PMID:17360625
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PMID:17355171
Hierarchical classification of functionally equivalent genes in prokaryotes. PMID:17353185
Structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1. PMID:17349044
Evaluation of the structural quality of modeled proteins by using globularity criteria. PMID:17346357
Comparison of protein structures by growing neighborhood alignments. PMID:17338826
Structure of 5-formyltetrahydrofolate cyclo-ligase from Bacillus anthracis (BA4489). PMID:17329806
Glycolipid transfer proteins. PMID:17320476
Long-term trends in evolution of indels in protein sequences. PMID:17298668
Protein structural variation in computational models and crystallographic data. PMID:17292835
Predicting zinc binding at the proteome level. PMID:17280606
Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry. PMID:17264128
Motif kernel generated by genetic programming improves remote homology and fold detection. PMID:17254344
Projections for fast protein structure retrieval. PMID:17254310
pH-tuneable binding of 2'-phospho-ADP-ribose to ketopantoate reductase: a structural and calorimetric study. PMID:17242510
Pyrimethamine as a potential pharmacological chaperone for late-onset forms of GM2 gangliosidosis. PMID:17237499
Protein and DNA sequence determinants of thermophilic adaptation. PMID:17222055
Improved Chou-Fasman method for protein secondary structure prediction. PMID:17217506
A consensus view of protein dynamics. PMID:17215349
A generalized analysis of hydrophobic and loop clusters within globular protein sequences. PMID:17210072
Towards alignment independent quantitative assessment of homology detection. PMID:17205117
W-motif exchange between beta-propeller proteins. PMID:17203392
Novel beta-barrel fold in the nuclear magnetic resonance structure of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus. PMID:17202208
SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. PMID:17202171
TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences. PMID:17199898
Prediction of amyloidogenic and disordered regions in protein chains. PMID:17196033
Evaluation of features for catalytic residue prediction in novel folds. PMID:17189479
Molecular evolution of peptide methionine sulfoxide reductases (MsrA and MsrB): on the early development of a mechanism that protects against oxidative damage. PMID:17180746
ERp57 is essential for efficient folding of glycoproteins sharing common structural domains. PMID:17170699
Modeling the evolution of protein domain architectures using maximum parsimony. PMID:17166515
EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies. PMID:17164525
The molecular structure of Rv1873, a conserved hypothetical protein from Mycobacterium tuberculosis, at 1.38 A resolution. PMID:17142896
Phospho3D: a database of three-dimensional structures of protein phosphorylation sites. PMID:17142231
Structural similarity enhances interaction propensity of proteins. PMID:17141268
Connectivity independent protein-structure alignment: a hierarchical approach. PMID:17118190
Molecular modeling and characterization of Vibrio cholerae transcription regulator HlyU. PMID:17116251
3D complex: a structural classification of protein complexes. PMID:17112313
The liganding of glycolipid transfer protein is controlled by glycolipid acyl structure. PMID:17105344
Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry. PMID:17098870
Structural modeling of protein interactions by analogy: application to PSD-95. PMID:17096593
Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level. PMID:17090320
The crystal structure of Arabidopsis thaliana allene oxide cyclase: insights into the oxylipin cyclization reaction. PMID:17085685
Longin-like folds identified in CHiPS and DUF254 proteins: vesicle trafficking complexes conserved in eukaryotic evolution. PMID:17075139
Characterization of two potentially universal turn motifs that shape the repeated five-residues fold--crystal structure of a lumenal pentapeptide repeat protein from Cyanothece 51142. PMID:17075135
A backbone-based theory of protein folding. PMID:17075053
Biosynthesis of phosphoserine in the Methanococcales. PMID:17071763
Divergent evolution of a structural proteome: phenomenological models. PMID:17071665
Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches. PMID:17068079
SISYPHUS--structural alignments for proteins with non-trivial relationships. PMID:17068077
TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method. PMID:17065464
Structural changes of bacteriophage phi29 upon DNA packaging and release. PMID:17053784
Representing and comparing protein structures as paths in three-dimensional space. PMID:17052359
A framework for protein structure classification and identification of novel protein structures. PMID:17042958
Building multiclass classifiers for remote homology detection and fold recognition. PMID:17042943
High-affinity binding of the staphylococcal HarA protein to haptoglobin and hemoglobin involves a domain with an antiparallel eight-stranded beta-barrel fold. PMID:17041047
Bayesian data mining of protein domains gives an efficient predictive algorithm and new insight. PMID:17028865
Predicting residue-wise contact orders in proteins by support vector regression. PMID:17014735
Ammonium recruitment and ammonia transport by E. coli ammonia channel AmtB. PMID:17012311
The many faces of protein-protein interactions: A compendium of interface geometry. PMID:17009862
Intricate knots in proteins: Function and evolution. PMID:16978047
Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection. PMID:16971460
Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction. PMID:16970830
TASSER-Lite: an automated tool for protein comparative modeling. PMID:16963505
Evolution of protein structural classes and protein sequence families. PMID:16959887
CRNPRED: highly accurate prediction of one-dimensional protein structures by large-scale critical random networks. PMID:16952323
Genetic analysis of MEFV gene pyrin domain in patients with Behçet's disease. PMID:16951489
MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information. PMID:16936316
MultiSeq: unifying sequence and structure data for evolutionary analysis. PMID:16914055
Anisotropic deformation response of single protein molecules. PMID:16908850
The structure of the endoribonuclease XendoU: From small nucleolar RNA processing to severe acute respiratory syndrome coronavirus replication. PMID:16895992
Protein structure database search and evolutionary classification. PMID:16885238
Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families. PMID:16882992
An amino acid "transmembrane tendency" scale that approaches the theoretical limit to accuracy for prediction of transmembrane helices: relationship to biological hydrophobicity. PMID:16877712
Genomic scale sub-family assignment of protein domains. PMID:16877569
A fast SCOP fold classification system using content-based E-Predict algorithm. PMID:16872501
A critical beta6-beta7 loop in the pleckstrin homology domain of ceramide kinase. PMID:16872273
Crystal structure of TDP-fucosamine acetyltransferase (WecD) from Escherichia coli, an enzyme required for enterobacterial common antigen synthesis. PMID:16855251
Crystal structure of a type III pantothenate kinase: insight into the mechanism of an essential coenzyme A biosynthetic enzyme universally distributed in bacteria. PMID:16855243
MANET: tracing evolution of protein architecture in metabolic networks. PMID:16854231
The family 42 carbohydrate-binding module of family 54 alpha-L-arabinofuranosidase specifically binds the arabinofuranose side chain of hemicellulose. PMID:16846393
OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structures. PMID:16845117
SNP@Domain: a web resource of single nucleotide polymorphisms (SNPs) within protein domain structures and sequences. PMID:16845090
KemaDom: a web server for domain prediction using kernel machine with local context. PMID:16844982
Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains. PMID:16844978
FISH--family identification of sequence homologues using structure anchored hidden Markov models. PMID:16844969
Tools for integrated sequence-structure analysis with UCSF Chimera. PMID:16836757
Purification, crystallization and preliminary X-ray diffraction analysis of RafE, a sugar-binding lipoprotein from Streptococcus pneumoniae. PMID:16820692
A limited universe of membrane protein families and folds. PMID:16815920
Comparison of a homology model and the crystallographic structure of human 11beta-hydroxysteroid dehydrogenase type 1 (11betaHSD1) in a structure-based identification of inhibitors. PMID:16783599
Structures of apo- and holo-tyrosine phenol-lyase reveal a catalytically critical closed conformation and suggest a mechanism for activation by K+ ions. PMID:16768450
Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification. PMID:16762072
High throughput profile-profile based fold recognition for the entire human proteome. PMID:16759376
Automated functional classification of experimental and predicted protein structures. PMID:16749925
Protein complex compositions predicted by structural similarity. PMID:16738133
Statistical limits to the identification of ion channel domains by sequence similarity. PMID:16735758
Protein family expansions and biological complexity. PMID:16733546
Structure-based function inference using protein family-specific fingerprints. PMID:16731985
Structural diversity of protein segments follows a power-law distribution. PMID:16731566
Discrete profile comparison using information bottleneck. PMID:16723011
Protein ranking by semi-supervised network propagation. PMID:16723003
Evidence from bioinformatics, expression and inhibition studies of phosphoinositide-3 kinase signalling in Giardia intestinalis. PMID:16707026
Optimizing amino acid substitution matrices with a local alignment kernel. PMID:16677385
Multipolar representation of protein structure. PMID:16674828
Crystal structure of hypothetical protein TTHB192 from Thermus thermophilus HB8 reveals a new protein family with an RNA recognition motif-like domain. PMID:16672237
Contribution of the mu loop to the structure and function of rat glutathione transferase M1-1. PMID:16672236
Identification of zinc-ligated cysteine residues based on 13Calpha and 13Cbeta chemical shift data. PMID:16645816
Characterization of the structure of RAMP1 by mutagenesis and molecular modeling. PMID:16632510
Fold-recognition and comparative modeling of human alpha2,3-sialyltransferases reveal their sequence and structural similarities to CstII from Campylobacter jejuni. PMID:16620397
ROC and confusion analysis of structure comparison methods identify the main causes of divergence from manual protein classification. PMID:16613604
Evolution of structural shape in bacterial globin-related proteins. PMID:16612536
Structural comparison of the two alternative transition states for folding of TI I27. PMID:16603501
A tale of two ferredoxins: sequence similarity and structural differences. PMID:16603087
A comparative study of available software for high-accuracy homology modeling: from sequence alignments to structural models. PMID:16600967
Structure of phage protein BC1872 from Bacillus cereus, a singleton with new fold. PMID:16596646
A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins. PMID:16585737
Expression, crystallization and preliminary X-ray crystallographic studies of the outer membrane protein OmpW from Escherichia coli. PMID:16582500
Protein secondary structure prediction for a single-sequence using hidden semi-Markov models. PMID:16571137
Structural proteomics of minimal organisms: conservation of protein fold usage and evolutionary implications. PMID:16566839
A method for finding candidate conformations for molecular replacement using relative rotation between domains of a known structure. PMID:16552141
Exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds. PMID:16549009
Spectral clustering of protein sequences. PMID:16547200
Domain-based small molecule binding site annotation. PMID:16545112
Structural basis for rodlet assembly in fungal hydrophobins. PMID:16537446
Identification of similar regions of protein structures using integrated sequence and structure analysis tools. PMID:16526955
The origins and evolution of functional modules: lessons from protein complexes. PMID:16524839
Towards genome-scale structure prediction for transmembrane proteins. PMID:16524835
Crystal structure of 3-hydroxyanthranilic acid 3,4-dioxygenase from Saccharomyces cerevisiae: a special subgroup of the type III extradiol dioxygenases. PMID:16522801
Identification of correct regions in protein models using structural, alignment, and consensus information. PMID:16522791
Hyaluronidases: their genomics, structures, and mechanisms of action. PMID:16522010
The first crystal structure of an archaeal helical repeat protein. PMID:16511116
A gold standard set of mechanistically diverse enzyme superfamilies. PMID:16507141
Structural and functional insights into the B30.2/SPRY domain. PMID:16498413
Human herpesvirus 1 UL24 gene encodes a potential PD-(D/E)XK endonuclease. PMID:16474163
On single and multiple models of protein families for the detection of remote sequence relationships. PMID:16448555
Identification and characterization of RbmA, a novel protein required for the development of rugose colony morphology and biofilm structure in Vibrio cholerae. PMID:16428409
Prediction of protein structural class with Rough Sets. PMID:16412240
The structure of Leishmania mexicana ICP provides evidence for convergent evolution of cysteine peptidase inhibitors. PMID:16407198
The structures of the thrombospondin-1 N-terminal domain and its complex with a synthetic pentameric heparin. PMID:16407063
A high level interface to SCOP and ASTRAL implemented in python. PMID:16403221
Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerases. PMID:16395333
FAMCS: finding all maximal common substructures in proteins. PMID:16393147
The evolutionary relationship of the domain architectures in the RhoGEF-containing proteins. PMID:16393146
Mutation of the LUNATIC FRINGE gene in humans causes spondylocostal dysostosis with a severe vertebral phenotype. PMID:16385447
Epitome: database of structure-inferred antigenic epitopes. PMID:16381978
DBD: a transcription factor prediction database. PMID:16381970
AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB. PMID:16381925
The Database of Macromolecular Motions: new features added at the decade mark. PMID:16381870
iMOTdb--a comprehensive collection of spatially interacting motifs in proteins. PMID:16381866
DMAPS: a database of multiple alignments for protein structures. PMID:16381863
MulPSSM: a database of multiple position-specific scoring matrices of protein domain families. PMID:16381855
SitesBase: a database for structure-based protein-ligand binding site comparisons. PMID:16381853
The REFOLD database: a tool for the optimization of protein expression and refolding. PMID:16381847
Frequencies of hydrophobic and hydrophilic runs and alternations in proteins of known structure. PMID:16373477
X-ray structure of engineered human Aortic Preferentially Expressed Protein-1 (APEG-1). PMID:16354304
Probabilistic annotation of protein sequences based on functional classifications. PMID:16354297
The crystal structure of CREG, a secreted glycoprotein involved in cellular growth and differentiation. PMID:16344469
The Unfinished Story of Cytochrome f. PMID:16328825
Protein surface analysis for function annotation in high-throughput structural genomics pipeline. PMID:16322579
The distance-profile representation and its application to detection of distantly related protein families. PMID:16316461
Identification of an Escherichia coli O157:H7 heme oxygenase with tandem functional repeats. PMID:16275907
Structural basis of severe acute respiratory syndrome coronavirus ADP-ribose-1''-phosphate dephosphorylation by a conserved domain of nsP3. PMID:16271890
Divergent evolution within protein superfolds inferred from profile-based phylogenetics. PMID:16266719
Evolution of an acylase active on cephalosporin C. PMID:16260759
Gene and genome duplication in Acanthamoeba polyphaga Mimivirus. PMID:16254344
A geometric construction determines all permissible strand arrangements of sandwich proteins. PMID:16249331
Structural characterization of proteins using residue environments. PMID:16245324
Structural evolution of the protein kinase-like superfamily. PMID:16244704
Statistical distributions of optimal global alignment scores of random protein sequences. PMID:16225696
Natural history of S-adenosylmethionine-binding proteins. PMID:16225687
Prediction of beta-barrel membrane proteins by searching for restricted domains. PMID:16225682
ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins. PMID:16225676
Protein database searches using compositionally adjusted substitution matrices. PMID:16218944
Structure of Ptr ToxA: an RGD-containing host-selective toxin from Pyrenophora tritici-repentis. PMID:16214901
Sequence and structural analysis of BTB domain proteins. PMID:16207353
Crystal structures and proposed structural/functional classification of three protozoan proteins from the isochorismatase superfamily. PMID:16199669
Structural genomics of the severe acute respiratory syndrome coronavirus: nuclear magnetic resonance structure of the protein nsP7. PMID:16188992
Evolutionary plasticity of protein families: coupling between sequence and structure variation. PMID:16184609
Insights into the quaternary association of proteins through structure graphs: a case study of lectins. PMID:16173917
A computational method to predict genetically encoded rare amino acids in proteins. PMID:16168086
Protein secondary structure assignment revisited: a detailed analysis of different assignment methods. PMID:16164759
Statistical signals in bioinformatics. PMID:16157888
COG3926 and COG5526: a tale of two new lysozyme-like protein families. PMID:16155206
Structural models for the protein family characterized by gamete surface protein Pfs230 of Plasmodium falciparum. PMID:16155126
RNA silencing suppressor p21 of Beet yellows virus forms an RNA binding octameric ring structure. PMID:16154094
GASH: an improved algorithm for maximizing the number of equivalent residues between two protein structures. PMID:16146579
DCCP and DICP: construction and analyses of databases for copper- and iron-chelating proteins. PMID:16144523
A protein domain interaction interface database: InterPare. PMID:16122378
Physics and evolution of thermophilic adaptation. PMID:16120678
Functional coverage of the human genome by existing structures, structural genomics targets, and homology models. PMID:16118666
Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different. PMID:16105176
Improving the precision of the structure-function relationship by considering phylogenetic context. PMID:16103910
PALSSE: a program to delineate linear secondary structural elements from protein structures. PMID:16095538
Characterization of carbohydrate-binding cytochrome b562 from the white-rot fungus Phanerochaete chrysosporium. PMID:16085848
Localization of protein-binding sites within families of proteins. PMID:16081657
Crystal structure of the bacterial YhcH protein indicates a role in sialic acid catabolism. PMID:16077096
Variations in plant metallothioneins: the heavy metal hyperaccumulator Thlaspi caerulescens as a study case. PMID:16052319
Structure, function, and evolution of transient and obligate protein-protein interactions. PMID:16043700
Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains. PMID:16040597
NMR data collection and analysis protocol for high-throughput protein structure determination. PMID:16027363
Nh3D: a reference dataset of non-homologous protein structures. PMID:16011803
A sequence sub-sampling algorithm increases the power to detect distant homologues. PMID:16006623
An inactivated nuclease-like domain in RecC with novel function: implications for evolution. PMID:15985153
CAMPO, SCR_FIND and CHC_FIND: a suite of web tools for computational structural biology. PMID:15980521
Protein structure prediction servers at University College London. PMID:15980489
FFAS03: a server for profile--profile sequence alignments. PMID:15980471
SCANMOT: searching for similar sequences using a simultaneous scan of multiple sequence motifs. PMID:15980468
Fragnostic: walking through protein structure space. PMID:15980462
The HHpred interactive server for protein homology detection and structure prediction. PMID:15980461
TMB-Hunt: a web server to screen sequence sets for transmembrane beta-barrel proteins. PMID:15980452
DIAL: a web-based server for the automatic identification of structural domains in proteins. PMID:15980441
PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families. PMID:15980440
Identification of novel restriction endonuclease-like fold families among hypothetical proteins. PMID:15972856
Epimerase active domain of Pseudomonas aeruginosa AlgG, a protein that contains a right-handed beta-helix. PMID:15968068
Structure-based functional identification of a novel heme-binding protein from Thermus thermophilus HB8. PMID:15965735
A test of enhancing model accuracy in high-throughput crystallography. PMID:15965733
DOM-fold: a structure with crossing loops found in DmpA, ornithine acetyltransferase, and molybdenum cofactor-binding domain. PMID:15937278
Structural and functional characterization of CFE88: evidence that a conserved and essential bacterial protein is a methyltransferase. PMID:15929997
1.6 A crystal structure of YteR protein from Bacillus subtilis, a predicted lyase. PMID:15906318
Universal sharing patterns in proteomes and evolution of protein fold architecture and life. PMID:15883883
Mechanically unfolding the small, topologically simple protein L. PMID:15863479
TM-align: a protein structure alignment algorithm based on the TM-score. PMID:15849316
Cloning, characterization and structural model of a FatA-type thioesterase from sunflower seeds (Helianthus annuus L.). PMID:15841386
All are not equal: a benchmark of different homology modeling programs. PMID:15840834
Structural similarity to bridge sequence space: finding new families on the bridges. PMID:15840833
A folding-dependent mechanism of antimicrobial peptide resistance to degradation unveiled by solution structure of distinctin. PMID:15840728
Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER. PMID:15831105
A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles. PMID:15819976
Visualization of conformational distribution of short to medium size segments in globular proteins and identification of local structural motifs. PMID:15802651
The P5 protein from bacteriophage phi-6 is a distant homolog of lytic transglycosylases. PMID:15802648
Columba: an integrated database of proteins, structures, and annotations. PMID:15801979
Comparative mapping of sequence-based and structure-based protein domains. PMID:15790427
Evolution of distinct EGF domains with specific functions. PMID:15772310
TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins. PMID:15769290
Exploring the common dynamics of homologous proteins. Application to the globin family. PMID:15749782
The critical role of disulfide bond formation in protein sorting in the endosperm of rice. PMID:15749763
Evolutionary profiles from the QR factorization of multiple sequence alignments. PMID:15741270
Global mapping of the protein structure space and application in structure-based inference of protein function. PMID:15705717
Symmetry and frustration in protein energy landscapes: a near degeneracy resolves the Rop dimer-folding mystery. PMID:15701699
Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. PMID:15701525
Proteins with two SUMO-like domains in chromatin-associated complexes: the RENi (Rad60-Esc2-NIP45) family. PMID:15698469
Availability of short amino acid sequences in proteins. PMID:15689510
ProbCons: Probabilistic consistency-based multiple sequence alignment. PMID:15687296
Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential. PMID:15673715
Predicted hexameric structure of the Agrobacterium VirB4 C terminus suggests VirB4 acts as a docking site during type IV secretion. PMID:15668378
Intramolecular disulphide bond arrangements in nonhomologous proteins. PMID:15659377
The protein structure prediction problem could be solved using the current PDB library. PMID:15653774
Crystal structure of the virulence gene activator AphA from Vibrio cholerae reveals it is a novel member of the winged helix transcription factor superfamily. PMID:15647287
Structure and intracellular targeting of the SARS-coronavirus Orf7a accessory protein. PMID:15642263
Protein conformational space in higher order phi-Psi maps. PMID:15640351
EDD, a novel phosphotransferase domain common to mannose transporter EIIA, dihydroxyacetone kinase, and DegV. PMID:15632288
Descriptor-based protein remote homology identification. PMID:15632283
Phylogeny determined by protein domain content. PMID:15630082
The path to enlightenment: making sense of genomic and proteomic information. PMID:15629052
GenDiS: Genomic Distribution of protein structural domain Superfamilies. PMID:15608190
S4: structure-based sequence alignments of SCOP superfamilies. PMID:15608181
A novel member of the YchN-like fold: solution structure of the hypothetical protein Tm0979 from Thermotoga maritima. PMID:15608123
Analysis of superfamily specific profile-profile recognition accuracy. PMID:15603591
4SCOPmap: automated assignment of protein structures to evolutionary superfamilies. PMID:15598351
A functional hierarchical organization of the protein sequence space. PMID:15596019
PreSPI: a domain combination based prediction system for protein-protein interaction. PMID:15576357
The VASP tetramerization domain is a right-handed coiled coil based on a 15-residue repeat. PMID:15569942
Protein family comparison using statistical models and predicted structural information. PMID:15563734
Molecular modelling prediction of ligand binding site flexibility. PMID:15562988
On the use of DXMS to produce more crystallizable proteins: structures of the T. maritima proteins TM0160 and TM1171. PMID:15557262
A model of the acid sphingomyelinase phosphoesterase domain based on its remote structural homolog purple acid phosphatase. PMID:15557261
Prediction of the structural motifs of sandwich proteins. PMID:15550537
Compound library development guided by protein structure similarity clustering and natural product structure. PMID:15548605
An analysis of core deformations in protein superfamilies. PMID:15542556
Extracting multiple structural alignments from pairwise alignments: a comparison of a rigorous and a heuristic approach. PMID:15531607
Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. PMID:15523666
The Molecular Pages of the mesotelencephalic dopamine consortium (DopaNet). PMID:15518589
Identification and functional verification of archaeal-type phosphoenolpyruvate carboxylase, a missing link in archaeal central carbohydrate metabolism. PMID:15516590
Evolutionarily conserved regions and hydrophobic contacts at the superfamily level: The case of the fold-type I, pyridoxal-5'-phosphate-dependent enzymes. PMID:15498941
To be folded or to be unfolded? PMID:15498936
Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation. PMID:15492216
Crystal structure of the YgfZ protein from Escherichia coli suggests a folate-dependent regulatory role in one-carbon metabolism. PMID:15489424
High-throughput computational and experimental techniques in structural genomics. PMID:15489337
Calcium-induced tertiary structure modifications of endo-beta-1,3-glucanase from Pyrococcus furiosus in 7.9 M guanidinium chloride. PMID:15482259
Helical packing patterns in membrane and soluble proteins. PMID:15465852
Crystallographic structure of the nuclease domain of 3'hExo, a DEDDh family member, bound to rAMP. PMID:15451662
The protein structures that shape caspase activity, specificity, activation and inhibition. PMID:15450003
PIN domain of Nob1p is required for D-site cleavage in 20S pre-rRNA. PMID:15388878
Analysis of protein homology by assessing the (dis)similarity in protein loop regions. PMID:15382231
Enhanced functional and structural domain assignments using remote similarity detection procedures for proteins encoded in the genome of Mycobacterium tuberculosis H37Rv. PMID:15381846
Reconstruction of ancestral protein sequences and its applications. PMID:15377393
Comparative homology agreement search: an effective combination of homology-search methods. PMID:15367730
Identifying DNA-binding proteins using structural motifs and the electrostatic potential. PMID:15356290
Molecular dimension explored in evolution to promote proteomic complexity. PMID:15347802
Rational proteomics II: electrostatic nature of cofactor preference in the short-chain oxidoreductase (SCOR) enzyme family. PMID:15340916
A complementary bioinformatics approach to identify potential plant cell wall glycosyltransferase-encoding genes. PMID:15333752
From endonucleases to transcription factors: evolution of the AP2 DNA binding domain in plants. PMID:15319480
Crystal structure of archaeal ribonuclease P protein Ph1771p from Pyrococcus horikoshii OT3: an archaeal homolog of eukaryotic ribonuclease P protein Rpp29. PMID:15317976
Crystal structure of the S-adenosylmethionine-dependent enzyme MoaA and its implications for molybdenum cofactor deficiency in humans. PMID:15317939
Approximate protein structural alignment in polynomial time. PMID:15304646
Structural analysis of the bipartite DNA-binding domain of Tc3 transposase bound to transposon DNA. PMID:15304566
Estimates of statistical significance for comparison of individual positions in multiple sequence alignments. PMID:15296518
Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1. PMID:15287974
Utility of homology models in the drug discovery process. PMID:15279849
A classification of disulfide patterns and its relationship to protein structure and function. PMID:15273305
Integrated web service for improving alignment quality based on segments comparison. PMID:15271224
Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point. PMID:15215530
Database searching by flexible protein structure alignment. PMID:15215527
Analysis of the "thermodynamic information content" of a Homo sapiens structural database reveals hierarchical thermodynamic organization. PMID:15215522
BSDD: Biomolecules Segment Display Device--a web-based interactive display tool. PMID:15215468
iMOT: an interactive package for the selection of spatially interacting motifs. PMID:15215459
FATCAT: a web server for flexible structure comparison and structure similarity searching. PMID:15215455
pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins. PMID:15215448
FoldMiner and LOCK 2: protein structure comparison and motif discovery on the web. PMID:15215444
PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction. PMID:15215441
SDPMOD: an automated comparative modeling server for small disulfide-bonded proteins. PMID:15215410
The dependence of all-atom statistical potentials on structural training database. PMID:15189839
Interaction profile-based protein classification of death domain. PMID:15189571
An overview of the basic helix-loop-helix proteins. PMID:15186484
Prediction of protein folding rates from the amino acid sequence-predicted secondary structure. PMID:15184682
Crystal structure of LeuA from Mycobacterium tuberculosis, a key enzyme in leucine biosynthesis. PMID:15159544
Frequency of gaps observed in a structurally aligned protein pair database suggests a simple gap penalty function. PMID:15155852
Scoring profile-to-profile sequence alignments. PMID:15152092
Solution structure of the hypothetical protein Mth677 from Methanobacterium thermoautotrophicum: a novel alpha+beta fold. PMID:15152082
Recognition of functional sites in protein structures. PMID:15147845
Sequence-structure mapping errors in the PDB: OB-fold domains. PMID:15133161
A Structural-informatics approach for tracing beta-sheets: building pseudo-C(alpha) traces for beta-strands in intermediate-resolution density maps. PMID:15123425
Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns. PMID:15121895
The modeling of the structure of the cysteine-rich domain of metabotropic glutamate receptors. PMID:15116561
SUPFAM: a database of sequence superfamilies of protein domains. PMID:15113407
Domain insertions in protein structures. PMID:15099733
Protein ranking: from local to global structure in the protein similarity network. PMID:15087500
New advances in normal mode analysis of supermolecular complexes and applications to structural refinement. PMID:15078222
Probable epitopes: Relationships between myelin basic protein antigenic determinants and viral and bacterial proteins. PMID:15067168
PASS2: an automated database of protein alignments organised as structural superfamilies. PMID:15059245
Solution structure of a novel calcium binding protein, MTH1880, from Methanobacterium thermoautotrophicum. PMID:15044740
A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications. PMID:15044734
MUSCLE: multiple sequence alignment with high accuracy and high throughput. PMID:15034147
Theoretical model of the three-dimensional structure of a sugar-binding protein from Pyrococcus horikoshii: structural analysis and sugar-binding simulations. PMID:15015939
The severe acute respiratory syndrome-coronavirus replicative protein nsp9 is a single-stranded RNA-binding subunit unique in the RNA virus world. PMID:15007178
Transmembrane protein domains rarely use covalent domain recombination as an evolutionary mechanism. PMID:14993608
Comparative analysis of protein domain organization. PMID:14993202
Local feature frequency profile: a method to measure structural similarity in proteins. PMID:14985506
Sensitivity and selectivity in protein structure comparison. PMID:14978311
The nonconserved wrapping of conserved protein folds reveals a trend toward increasing connectivity in proteomic networks. PMID:14978274
Crystal structure of Mycoplasma arthritidis mitogen complexed with HLA-DR1 reveals a novel superantigen fold and a dimerized superantigen-MHC complex. PMID:14962388
Correlation between sequence hydrophobicity and surface-exposure pattern of database proteins. PMID:14767075
Protein structure prediction using sparse dipolar coupling data. PMID:14744980
Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme. PMID:14704425
An optimal structure-discriminative amino acid index for protein fold recognition. PMID:14695283
On hydrophobicity and conformational specificity in proteins. PMID:14695246
The crystal structure of Pseudomonas avirulence protein AvrPphB: a papain-like fold with a distinct substrate-binding site. PMID:14694194
Improvement of comparative modeling by the application of conserved motifs amongst distantly related proteins as additional restraints. PMID:14691673
FoldMiner: structural motif discovery using an improved superposition algorithm. PMID:14691242
TOPS: an enhanced database of protein structural topology. PMID:14681405
The SUPERFAMILY database in 2004: additions and improvements. PMID:14681402
SCOP database in 2004: refinements integrate structure and sequence family data. PMID:14681400
The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms. PMID:14681393
DomIns: a web resource for domain insertions in known protein structures. PMID:14681392
The ASTRAL Compendium in 2004. PMID:14681391
On the evolution of structure in aminoacyl-tRNA synthetases. PMID:14665676
Multi-domain protein families and domain pairs: comparison with known structures and a random model of domain recombination. PMID:14649290
LCN6, a novel human epididymal lipocalin. PMID:14617364
PCAS--a precomputed proteome annotation database resource. PMID:14594458
Protein evolution within a structural space. PMID:14581198
CASP5 target classification. PMID:14579323
Multiple structural alignment by secondary structures: algorithm and applications. PMID:14573862
On the properties and sequence context of structurally ambivalent fragments in proteins. PMID:14573856
OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy. PMID:14552658
Visualisation and graph-theoretic analysis of a large-scale protein structural interactome. PMID:14531933
Crystal structure of Escherichia coli protein ybgI, a toroidal structure with a dinuclear metal site. PMID:14519207
Structure and mechanism of a bacterial haloalcohol dehalogenase: a new variation of the short-chain dehydrogenase/reductase fold without an NAD(P)H binding site. PMID:14517233
Molecular modelling of S1 and S2 subunits of SARS coronavirus spike glycoprotein. PMID:14511651
Exploring the sequence-structure protein landscape in the glycosyltransferase family. PMID:14500887
Profile-profile comparisons by COMPASS predict intricate homologies between protein families. PMID:14500884
A consensus view of fold space: combining SCOP, CATH, and the Dali Domain Dictionary. PMID:14500873
Using protein design for homology detection and active site searches. PMID:12975528
ELISA: structure-function inferences based on statistically significant and evolutionarily inspired observations. PMID:12952559
Crystal structure of the YajQ protein from Haemophilus influenzae reveals a tandem of RNP-like domains. PMID:12943362
Rationally selected basis proteins: a new approach to selecting proteins for spectroscopic secondary structure analysis. PMID:12931000
Homology modeling provides insights into the binding mode of the PAAD/DAPIN/pyrin domain, a fourth member of the CARD/DD/DED domain family. PMID:12930987
Funnel sculpting for in silico assembly of secondary structure elements of proteins. PMID:12925740
An evolutionarily structured universe of protein architecture. PMID:12840035
Comparative analysis of the Escherichia coli ketopantoate hydroxymethyltransferase crystal structure confirms that it is a member of the (betaalpha)8 phosphoenolpyruvate/pyruvate superfamily. PMID:12837791
Crystal structure of a putative methyltransferase from Mycobacterium tuberculosis: misannotation of a genome clarified by protein structural analysis. PMID:12837779
Crystal structure of the YchF protein reveals binding sites for GTP and nucleic acid. PMID:12837776
HPr kinase/phosphorylase, the sensor enzyme of catabolite repression in Gram-positive bacteria: structural aspects of the enzyme and the complex with its protein substrate. PMID:12837773
Pretty good guessing: protein structure prediction at CASP5. PMID:12837771
Characterization and prediction of linker sequences of multi-domain proteins by a neural network. PMID:12836673
Solution structure of Vibrio cholerae protein VC0424: a variation of the ferredoxin-like fold. PMID:12824501
Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures. PMID:12824322
Exploration of the cell-cycle genes found within the RIKEN FANTOM2 data set. PMID:12819135
Mouse proteome analysis. PMID:12819131
Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. PMID:12805271
Using structural motif templates to identify proteins with DNA binding function. PMID:12771208
Reducing the computational complexity of protein folding via fragment folding and assembly. PMID:12761388
Presence and expression of hydrogenase specific C-terminal endopeptidases in cyanobacteria. PMID:12735794
Peptidase family U34 belongs to the superfamily of N-terminal nucleophile hydrolases. PMID:12717035
A network of rice genes associated with stress response and seed development. PMID:12684538
Prediction of protein domain boundaries from sequence alone. PMID:12649427
A global representation of the protein fold space. PMID:12606708
Nucleic acid recognition by OB-fold proteins. PMID:12598368
Hydrophobicity of transmembrane proteins: spatially profiling the distribution. PMID:12592029
X-ray structure of the AAC(6')-Ii antibiotic resistance enzyme at 1.8 A resolution; examination of oligomeric arrangements in GNAT superfamily members. PMID:12592013
Evolution of transcription factors and the gene regulatory network in Escherichia coli. PMID:12582243
Crystal structure of the plasmid maintenance system epsilon/zeta: functional mechanism of toxin zeta and inactivation by epsilon 2 zeta 2 complex formation. PMID:12571357
Packing helices in proteins by global optimization of a potential energy function. PMID:12571353
Identification of a novel Bardet-Biedl syndrome protein, BBS7, that shares structural features with BBS1 and BBS2. PMID:12567324
Prediction algorithm for amino acid types with their secondary structure in proteins (PLATON) using chemical shifts. PMID:12566998
Improving the performance of DomainParser for structural domain partition using neural network. PMID:12560490
The alternating ATPase domains of MutS control DNA mismatch repair. PMID:12554674
Crystal structure of a trimeric form of dephosphocoenzyme A kinase from Escherichia coli. PMID:12538896
Finding weak similarities between proteins by sequence profile comparison. PMID:12527777
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003. PMID:12520060
Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database. PMID:12520058
MolMovDB: analysis and visualization of conformational change and structural flexibility. PMID:12520056
E-MSD: the European Bioinformatics Institute Macromolecular Structure Database. PMID:12520052
The esterase and PHD domains in CR1-like non-LTR retrotransposons. PMID:12519904
Automatic classification of protein structure by using Gauss integrals. PMID:12506205
POTE, a highly homologous gene family located on numerous chromosomes and expressed in prostate, ovary, testis, placenta, and prostate cancer. PMID:12475935
Structure of Bacillus subtilis YXKO--a member of the UPF0031 family and a putative kinase. PMID:12457846
The catalytic domains of thiamine triphosphatase and CyaB-like adenylyl cyclase define a novel superfamily of domains that bind organic phosphates. PMID:12456267
Total sequence decomposition distinguishes functional modules, "molegos" in apurinic/apyrimidinic endonucleases. PMID:12445335
Extension of a local backbone description using a structural alphabet: a new approach to the sequence-structure relationship. PMID:12441385
Definition of the tempo of sequence diversity across an alignment and automatic identification of sequence motifs: Application to protein homologous families and superfamilies. PMID:12441381
Rapid protein domain assignment from amino acid sequence using predicted secondary structure. PMID:12441380
Thoroughly sampling sequence space: large-scale protein design of structural ensembles. PMID:12441379
Transmembrane helix predictions revisited. PMID:12441377
The palm subdomain-based active site is internally permuted in viral RNA-dependent RNA polymerases of an ancient lineage. PMID:12421558
Protein folding in the post-genomic era. PMID:12417049
Analysis of protein sequence/structure similarity relationships. PMID:12414710
Structural basis for the oxidation of thiosulfate by a sulfur cycle enzyme. PMID:12411478
Helicobacter pylori expresses an autolytic enzyme: gene identification, cloning, and theoretical protein structure. PMID:12399497
Common features in structures and sequences of sandwich-like proteins. PMID:12384574
Expanding protein universe and its origin from the biological Big Bang. PMID:12384571
MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. PMID:12381844
Sequence variations within protein families are linearly related to structural variations. PMID:12381308
A comparison of profile hidden Markov model procedures for remote homology detection. PMID:12364612
Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins. PMID:12324397
High resolution crystal structure of domain I of the Saccharomyces cerevisiae homing endonuclease PI-SceI. PMID:12235380
Human members of the eukaryotic protein kinase family. PMID:12225582
Exploring the propensities of helices in PrP(C) to form beta sheet using NMR structures and sequence alignments. PMID:12202354
A structurally conserved water molecule in Rossmann dinucleotide-binding domains. PMID:12192068
Designability of alpha-helical proteins. PMID:12177419
Design of an optimal Chebyshev-expanded discrimination function for globular proteins. PMID:12142455
Thermodynamic environments in proteins: fundamental determinants of fold specificity. PMID:12142449
TRILOGY: Discovery of sequence-structure patterns across diverse proteins. PMID:12084910
In search for more accurate alignments in the twilight zone. PMID:12070323
Crystal structure of auxin-binding protein 1 in complex with auxin. PMID:12065401
Comparison of the small molecule metabolic enzymes of Escherichia coli and Saccharomyces cerevisiae. PMID:12045145
Homology induction: the use of machine learning to improve sequence similarity searches. PMID:11972320
Structural similarity to link sequence space: new potential superfamilies and implications for structural genomics. PMID:11967367
Structural genomics: a pipeline for providing structures for the biologist. PMID:11910018
Fold prediction of helical proteins using torsion angle dynamics and predicted restraints. PMID:11904420
PATE, a gene expressed in prostate cancer, normal prostate, and testis, identified by a functional genomic approach. PMID:11880645
Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation. PMID:11880627
Classification of protein folds. PMID:11876296
Breaking the singleton of germination protease. PMID:11847292
Conserved and nonconserved features of the folding pathway of hisactophilin, a beta-trefoil protein. PMID:11847289
Improved detection of homologous membrane proteins by inclusion of information from topology predictions. PMID:11847287
Mechanism of action and NAD+-binding mode revealed by the crystal structure of L-histidinol dehydrogenase. PMID:11842181
Crystal structure of the stimulatory complex of GTP cyclohydrolase I and its feedback regulatory protein GFRP. PMID:11818540
Crystal structure of the GABA(A)-receptor-associated protein, GABARAP. PMID:11818336
Protein topology and stability define the space of allowed sequences. PMID:11805293
Recursive domains in proteins. PMID:11790851
A comparison of position-specific score matrices based on sequence and structure alignments. PMID:11790846
Persistently conserved positions in structurally similar, sequence dissimilar proteins: roles in preserving protein fold and function. PMID:11790845
The CATH extended protein-family database: providing structural annotations for genome sequences. PMID:11790833
Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. PMID:11790828
BETAWRAP: successful prediction of parallel beta -helices from primary sequence reveals an association with many microbial pathogens. PMID:11752429
SCOR: a Structural Classification of RNA database. PMID:11752346
GTOP: a database of protein structures predicted from genome sequences. PMID:11752318
SUPFAM--a database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: implications for structural genomics and function annotation in genomes. PMID:11752317
PASS2: a semi-automated database of protein alignments organised as structural superfamilies. PMID:11752316
The Pfam protein families database. PMID:11752314
SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments. PMID:11752312
SCOP database in 2002: refinements accommodate structural genomics. PMID:11752311
ASTRAL compendium enhancements. PMID:11752310
Crystal structure of the fission yeast mitochondrial Holliday junction resolvase Ydc2. PMID:11726496
Structural genomics: an approach to the protein folding problem. PMID:11717420
Protein threading by learning. PMID:11717394
Identification of essential amino acids in the Azorhizobium caulinodans fucosyltransferase NodZ. PMID:11717264
The 2.0-A crystal structure of tachylectin 5A provides evidence for the common origin of the innate immunity and the blood coagulation systems. PMID:11707569
Crystal structure of human uroporphyrinogen III synthase. PMID:11689424
DIAN: a novel algorithm for genome ontological classification. PMID:11591654
Annotation transfer for genomics: measuring functional divergence in multi-domain proteins. PMID:11591640
A study of quality measures for protein threading models. PMID:11545673
The PYRIN domain: a member of the death domain-fold superfamily. PMID:11514682
Circularly permuted proteins in the protein structure database. PMID:11514678
NMR of hydrogen bonding in cold-shock protein A and an analysis of the influence of crystallographic resolution on comparisons of hydrogen bond lengths. PMID:11514676
A cofactor-dependent phosphoglycerate mutase homolog from Bacillus stearothermophilus is actually a broad specificity phosphatase. PMID:11514674
Molecular dynamics force probe simulations of antibody/antigen unbinding: entropic control and nonadditivity of unbinding forces. PMID:11509346
A sequence and structural study of transmembrane helices. PMID:11495225
X-ray structure of HPr kinase: a bacterial protein kinase with a P-loop nucleotide-binding domain. PMID:11483495
Support vector machines for predicting protein structural class. PMID:11483157
Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate. PMID:11447104
SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics. PMID:11433035
Classification of protein disulphide-bridge topologies. PMID:11394740
The structures of anthranilate synthase of Serratia marcescens crystallized in the presence of (i) its substrates, chorismate and glutamine, and a product, glutamate, and (ii) its end-product inhibitor, L-tryptophan. PMID:11371633
Tilt, twist, and coiling in beta-barrel membrane proteins: relation to infrared dichroism. PMID:11371453
Homology modelling and structural analysis of human arylamine N-acetyltransferase NAT1: evidence for the conservation of a cysteine protease catalytic domain and an active-site loop. PMID:11368758
Thermodynamic propensities of amino acids in the native state ensemble: implications for fold recognition. PMID:11316884
Frequencies of amino acid strings in globular protein sequences indicate suppression of blocks of consecutive hydrophobic residues. PMID:11316883
Hydrophobic moments of protein structures: spatially profiling the distribution. PMID:11309489
PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information. PMID:11292848
Treble clef finger--a functionally diverse zinc-binding structural motif. PMID:11292843
The Hans Neurath Award lecture of The Protein Society: proteins-- a testament to physics, chemistry, and evolution. PMID:11266588
ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches. PMID:11266569
Including biological literature improves homology search. PMID:11262956
Crystal structure of outer surface protein C (OspC) from the Lyme disease spirochete, Borrelia burgdorferi. PMID:11230121
Automated search of natively folded protein fragments for high-throughput structure determination in structural genomics. PMID:11206052
Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome. PMID:11160906
KH domain: one motif, two folds. PMID:11160884
Anisotropy of fluctuation dynamics of proteins with an elastic network model. PMID:11159421
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB). PMID:11125096
PALI-a database of Phylogeny and ALIgnment of homologous protein structures. PMID:11125050
Crystal structures of Mycobacterium tuberculosis RecA and its complex with ADP-AlF(4): implications for decreased ATPase activity and molecular aggregation. PMID:11121488
Accurate prediction of protein functional class from sequence in the Mycobacterium tuberculosis and Escherichia coli genomes using data mining. PMID:11119305
An overview of the structures of protein-DNA complexes. PMID:11104519
Crystal structure of the peptidyl-cysteine decarboxylase EpiD complexed with a pentapeptide substrate. PMID:11101502
Paired Ig-like receptor homologs in birds and mammals share a common ancestor with mammalian Fc receptors. PMID:11078516
Crystal structure of Streptococcus pneumoniae acyl carrier protein synthase: an essential enzyme in bacterial fatty acid biosynthesis. PMID:11032795
X-ray crystal structure of rabbit N-acetylglucosaminyltransferase I: catalytic mechanism and a new protein superfamily. PMID:11032794
Crystal structure of FadR, a fatty acid-responsive transcription factor with a novel acyl coenzyme A-binding fold. PMID:11013219
Reengineering the glutathione S-transferase scaffold: a rational design strategy pays off. PMID:10984526
Use of residue pairs in protein sequence-sequence and sequence-structure alignments. PMID:10975579
Improving the quality of twilight-zone alignments. PMID:10975570
Structural basis of the membrane-targeting and unmasking mechanisms of the radixin FERM domain. PMID:10970839
Homology modeling and characterization of IgE binding epitopes of mountain cedar allergen Jun a 3. PMID:10969020
Novel folded protein domains generated by combinatorial shuffling of polypeptide segments. PMID:10954734
Proteomics of Mycoplasma genitalium: identification and characterization of unannotated and atypical proteins in a small model genome. PMID:10931922
Essential motions and energetic contributions of individual residues in a peptide bound to an SH3 domain. PMID:10919999
Common fold in helix-hairpin-helix proteins. PMID:10908318
Two tricks in one bundle: helix-turn-helix gains enzymatic activity. PMID:10871343
Structural basis for the heterodimeric interaction between the acute leukaemia-associated transcription factors AML1 and CBFbeta. PMID:10856244
Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels. PMID:10854412
High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry. PMID:10811876
Simultaneous determination of disulphide bridge topology and three-dimensional structure using ambiguous intersulphur distance restraints: possibilities and limitations. PMID:10805126
Estimating the probability for a protein to have a new fold: A statistical computational model. PMID:10792051
Optimal region of average side-chain entropy for fast protein folding. PMID:10752620
Expectations from structural genomics. PMID:10739263
The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework. PMID:10734184
Proteins with similar architecture exhibit similar large-scale dynamic behavior. PMID:10733987
Microscopic stability of cold shock protein A examined by NMR native state hydrogen exchange as a function of urea and trimethylamine N-oxide. PMID:10716181
Comparison of sequence profiles. Strategies for structural predictions using sequence information. PMID:10716175
Selecting protein targets for structural genomics of Pyrobaculum aerophilum: validating automated fold assignment methods by using binary hypothesis testing. PMID:10706641
Environment-dependent residue contact energies for proteins. PMID:10706611
Crystal structure of ribosomal protein L4 shows RNA-binding sites for ribosome incorporation and feedback control of the S10 operon. PMID:10698923
Backbone dipoles generate positive potentials in all proteins: origins and implications of the effect. PMID:10692303
Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins. PMID:10684945
Thermolysin and mitochondrial processing peptidase: how far structure-functional convergence goes. PMID:10595562
SCOP: a structural classification of proteins database. PMID:10592240
The ASTRAL compendium for protein structure and sequence analysis. PMID:10592239
The Protein Data Bank. PMID:10592235
Detection of protein fold similarity based on correlation of amino acid properties. PMID:10588703
Crystal structure of penicillin G acylase from the Bro1 mutant strain of Providencia rettgeri. PMID:10548042
Solution structure of the receptor tyrosine kinase EphB2 SAM domain and identification of two distinct homotypic interaction sites. PMID:10548040
Diversity of functions of proteins with internal symmetry in spatial arrangement of secondary structural elements. PMID:10386871
The immunoglobulin-like modules Cepsilon3 and alpha2 are the minimal units necessary for human IgE-FcepsilonRI interaction. PMID:10359566
Feasibility in the inverse protein folding protocol. PMID:10338011
Factors limiting the performance of prediction-based fold recognition methods. PMID:10211821
CORA--topological fingerprints for protein structural families. PMID:10211816
Structural comparisons of TIM barrel proteins suggest functional and evolutionary relationships between beta-galactosidase and other glycohydrolases. PMID:10210191
Crystal structure of the HLA-Cw3 allotype-specific killer cell inhibitory receptor KIR2DL2. PMID:10097129
Crystal structure of human p32, a doughnut-shaped acidic mitochondrial matrix protein. PMID:10097078
Comparison of protein-protein interactions in serine protease-inhibitor and antibody-antigen complexes: implications for the protein docking problem. PMID:10091663
Analysis of zinc binding sites in protein crystal structures. PMID:10082367
The three-dimensional structure of the RNA-binding domain of ribosomal protein L2; a protein at the peptidyl transferase center of the ribosome. PMID:10075918
Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting distance geometry calculations of beta-sheet formation in proteins. PMID:10048326
The case for a common ancestor: kinesin and myosin motor proteins and G proteins. PMID:10047987
An intriguing controversy over protein structural class prediction. PMID:9988519
The structure of a PKD domain from polycystin-1: implications for polycystic kidney disease. PMID:9889186
Expanding yeast knowledge online. PMID:9885151
Structural basis for the recognition of superantigen streptococcal pyrogenic exotoxin A (SpeA1) by MHC class II molecules and T-cell receptors. PMID:9878045
Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements. PMID:9843945
HOMSTRAD: a database of protein structure alignments for homologous families. PMID:9828015
Singular points of protein beta-sheets. PMID:9827998
Effects of proline cis-trans isomerization on TB domain secondary structure. PMID:9792099
A database of macromolecular motions. PMID:9722650
Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. PMID:9722641
A C-terminal helicase domain of the human papillomavirus E1 protein binds E2 and the DNA polymerase alpha-primase p68 subunit. PMID:9696837
Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. PMID:9600919
A unified statistical framework for sequence comparison and structure comparison. PMID:9600892
Highly specific protein sequence motifs for genome analysis. PMID:9600885
Predicting amino acid sequences of the antibody human VH chains from its first several residues. PMID:9560252
Are protein folds atypical? PMID:9560215
Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins. PMID:9521122
Domain assignment for protein structures using a consensus approach: characterization and analysis. PMID:9521098
Seeking an ancient enzyme in Methanococcus jannaschii using ORF, a program based on predicted secondary structure comparisons. PMID:9501173
Synapsin I is structurally similar to ATP-utilizing enzymes. PMID:9463376
Simulating the minimum core for hydrophobic collapse in globular proteins. PMID:9416609
Touring protein fold space with Dali/FSSP. PMID:9399863
The PRINTS protein fingerprint database in its fifth year. PMID:9399860
SGD: Saccharomyces Genome Database. PMID:9399804
Anatomy of a conformational transition of beta-strand 6 in soybean beta-amylase caused by substrate (or inhibitor) binding to the catalytical site. PMID:9385643
TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. PMID:9385633
Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium. PMID:9342339
A structural census of the current population of protein sequences. PMID:9342336
Structural motifs at protein-protein interfaces: protein cores versus two-state and three-state model complexes. PMID:9300480
Aerolysin and pertussis toxin share a common receptor-binding domain. PMID:9218785
A proposed architecture for the central domain of the bacterial enhancer-binding proteins based on secondary structure prediction and fold recognition. PMID:9070437
SCOP: a structural classification of proteins database. PMID:9016544
Dali/FSSP classification of three-dimensional protein folds. PMID:9016542
Novel developments with the PRINTS protein fingerprint database. PMID:9016538
LPFC: an Internet library of protein family core structures. PMID:9007997
Folding of the N-terminal, ligand-binding region of integrin alpha-subunits into a beta-propeller domain. PMID:8990162
Sequence analysis of eukaryotic developmental proteins: ancient and novel domains. PMID:8889542
Xylanase homology modeling using the inverse protein folding approach. PMID:8845760
Self-consistently optimized statistical mechanical energy functions for sequence structure alignment. PMID:8762136
Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases. PMID:8762132
Sequence of bovine carbonic anhydrase VI: potential recognition sites for N-acetylgalactosaminyltransferase. PMID:8761494
Location of a potential transport binding site in a sigma class glutathione transferase by x-ray crystallography. PMID:8710848
Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites. PMID:8610096
Protein structures from domain packing--a game of twenty questions? PMID:8599626
The FSSP database: fold classification based on structure-structure alignment of proteins. PMID:8594580
Data growth and its impact on the SCOP database: new developments PubMed citations: 477.

477 articles citing: Data growth and its impact on the SCOP database: new developments

A consensus view of the proteome of the last universal common ancestor. PMID:35784055
The Structural Rule Distinguishing a Superfold: A Case Study of Ferredoxin Fold and the Reverse Ferredoxin Fold. PMID:35684484
A Computational Model for the PLP-Dependent Enzyme Methionine γ-Lyase. PMID:35558556
SCOPe: improvements to the structural classification of proteins - extended database to facilitate variant interpretation and machine learning. PMID:34850923
Structural dynamics in the evolution of a bilobed protein scaffold. PMID:34845009
A secondary structure-based position-specific scoring matrix applied to the improvement in protein secondary structure prediction. PMID:34320027
Critical assessment of coiled-coil predictions based on protein structure data. PMID:34127723
Ecology and molecular targets of hypermutation in the global microbiome. PMID:34031405
On the use of direct-coupling analysis with a reduced alphabet of amino acids combined with super-secondary structure motifs for protein fold prediction. PMID:33937764
The ranging of amino acids substitution matrices of various types in accordance with the alignment accuracy criterion. PMID:32921315
The Neighboring Subunit Is Engaged to Stabilize the Substrate in the Active Site of Plant Arginases. PMID:32754173
A physics-based energy function allows the computational redesign of a PDZ domain. PMID:32636412
Alzheimer's Disease: The Role of Mutations in Protein Folding. PMID:32468481
Prediction of Protein Tertiary Structure via Regularized Template Classification Techniques. PMID:32466409
Bacterial Origin and Reductive Evolution of the CPR Group. PMID:32031619
FTIP: an accurate and efficient method for global protein surface comparison. PMID:32022843
PhoH2 proteins couple RNA helicase and RNAse activities. PMID:31886915
Prediction of impacts of mutations on protein structure and interactions: SDM, a statistical approach, and mCSM, using machine learning. PMID:31693276
The CLN3 gene and protein: What we know. PMID:31568712
HH-suite3 for fast remote homology detection and deep protein annotation. PMID:31521110
Novel Inhibitory Function of the Rhizomucor miehei Lipase Propeptide and Three-Dimensional Structures of Its Complexes with the Enzyme. PMID:31460089
An NMR and MD study of complexes of bacteriophage lambda lysozyme with tetra- and hexa-N-acetylchitohexaose. PMID:31294851
ECOD: identification of distant homology among multidomain and transmembrane domain proteins. PMID:31226926
Wheat wounding-responsive HD-Zip IV transcription factor GL7 is predominantly expressed in grain and activates genes encoding defensins. PMID:31183604
Plasmodium pseudo-Tyrosine Kinase-like binds PP1 and SERA5 and is exported to host erythrocytes. PMID:31148576
rstoolbox - a Python library for large-scale analysis of computational protein design data and structural bioinformatics. PMID:31092198
The Origin and Evolution of Release Factors: Implications for Translation Termination, Ribosome Rescue, and Quality Control Pathways. PMID:31018531
Testing Empirical Support for Evolutionary Models that Root the Tree of Life. PMID:30887086
PFDB: A standardized protein folding database with temperature correction. PMID:30733462
A benchmark study of sequence alignment methods for protein clustering. PMID:30598070
Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes. PMID:30538677
SCOPe: classification of large macromolecular structures in the structural classification of proteins-extended database. PMID:30500919
SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins. PMID:30445541
A planarian nidovirus expands the limits of RNA genome size. PMID:30383829
The Pfam protein families database in 2019. PMID:30357350
Contributions of substitutions and indels to the structural variations in ancient protein superfamilies. PMID:30355304
Searching ECOD for Homologous Domains by Sequence and Structure. PMID:30040199
BIPSPI: a method for the prediction of partner-specific protein-protein interfaces. PMID:30020406
Crystal structure of the Streptococcus agalactiae CAMP factor provides insights into its membrane-permeabilizing activity. PMID:29884770
Nonnative Energetic Frustrations in Protein Folding at Residual Level: A Simulation Study of Homologous Immunoglobulin-like β-Sandwich Proteins. PMID:29783701
Structural biology data archiving - where we are and what lies ahead. PMID:29749603
HMMER Cut-off Threshold Tool (HMMERCTTER): Supervised classification of superfamily protein sequences with a reliable cut-off threshold. PMID:29579071
Evaluation of variability in high-resolution protein structures by global distance scoring. PMID:29560428
Structure function relations in PDZ-domain-containing proteins: Implications for protein networks in cellular signalling. PMID:29485124
Derivative-free neural network for optimizing the scoring functions associated with dynamic programming of pairwise-profile alignment. PMID:29467815
CIPPN: computational identification of protein pupylation sites by using neural network. PMID:29312575
Protein 3D Structure and Electron Microscopy Map Retrieval Using 3D-SURFER2.0 and EM-SURFER. PMID:29220075
Do Viruses Exchange Genes across Superkingdoms of Life? PMID:29163404
Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites. PMID:29106569
Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths. PMID:29078314
Interdependence, Reflexivity, Fidelity, Impedance Matching, and the Evolution of Genetic Coding. PMID:29077934
On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures. PMID:29028891
Thermal stability of pepsin: A predictive thermodynamic model of a multi-domain protein. PMID:28956016
NSiteMatch: Prediction of Binding Sites of Nucleotides by Identifying the Structure Similarity of Local Surface Patches. PMID:28811833
Crystal Structure of the DNA-Binding Domain of Human Herpesvirus 6A Immediate Early Protein 2. PMID:28794035
Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE. PMID:28784764
Predictions of Backbone Dynamics in Intrinsically Disordered Proteins Using De Novo Fragment-Based Protein Structure Predictions. PMID:28765603
Exploring general-purpose protein features for distinguishing enzymes and non-enzymes within the twilight zone. PMID:28732462
Phylogenetic Tracings of Proteome Size Support the Gradual Accretion of Protein Structural Domains and the Early Origin of Viruses from Primordial Cells. PMID:28690608
Resurrecting the Dead (Molecules). PMID:28652896
New Disulfide-Stabilized Fold Provides Sea Anemone Peptide to Exhibit Both Antimicrobial and TRPA1 Potentiating Properties. PMID:28468269
The Lon protease-like domain in the bacterial RecA paralog RadA is required for DNA binding and repair. PMID:28432121
Cooperativity and modularity in protein folding. PMID:28409080
Biocuration in the structure-function linkage database: the anatomy of a superfamily. PMID:28365730
Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification. PMID:28344575
Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions. PMID:28280526
An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins. PMID:28187133
Structure of the 40S ribosomal subunit of Plasmodium falciparum by homology and de novo modeling. PMID:28119814
Protein structure determination using metagenome sequence data. PMID:28104891
Structure of the acetophenone carboxylase core complex: prototype of a new class of ATP-dependent carboxylases/hydrolases. PMID:28054554
Arguments Reinforcing the Three-Domain View of Diversified Cellular Life. PMID:28050162
Sixty-five years of the long march in protein secondary structure prediction: the final stretch? PMID:28040746
Alpha Helices Are More Robust to Mutations than Beta Strands. PMID:27935949
SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins - extended Database. PMID:27914894
InterPro in 2017-beyond protein family and domain annotations. PMID:27899635
ECOD: new developments in the evolutionary classification of domains. PMID:27899594
Three-Dimensional Biologically Relevant Spectrum (BRS-3D): Shape Similarity Profile Based on PDB Ligands as Molecular Descriptors. PMID:27869685
Structural Interface Forms and Their Involvement in Stabilization of Multidomain Proteins or Protein Complexes. PMID:27763556
ProtNN: fast and accurate protein 3D-structure classification in structural and topological space. PMID:27688811
Development of a motif-based topology-independent structure comparison method to identify evolutionarily related folds. PMID:27671894
A new definition and properties of the similarity value between two protein structures. PMID:27623799
The centrosomal deubiquitylase USP21 regulates Gli1 transcriptional activity and stability. PMID:27621083
Evaluating the accuracy of protein design using native secondary sub-structures. PMID:27597167
Molecular Models of STAT5A Tetramers Complexed to DNA Predict Relative Genome-Wide Frequencies of the Spacing between the Two Dimer Binding Motifs of the Tetramer Binding Sites. PMID:27537504
Flavoprotein-Mediated Tellurite Reduction: Structural Basis and Applications to the Synthesis of Tellurium-Containing Nanostructures. PMID:27507969
The archiving and dissemination of biological structure data. PMID:27450113
Lessons from making the Structural Classification of Proteins (SCOP) and their implications for protein structure modelling. PMID:27284063
Dali server update. PMID:27131377
Impact of structure space continuity on protein fold classification. PMID:27006112
Classification of proteins with shared motifs and internal repeats in the ECOD database. PMID:26833690
Legionella pneumophila S1P-lyase targets host sphingolipid metabolism and restrains autophagy. PMID:26831115
DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions. PMID:26827237
The role of negative selection in protein evolution revealed through the energetics of the native state ensemble. PMID:26800099
Prediction and characterization of protein-protein interaction network in Bacillus licheniformis WX-02. PMID:26782814
New Dynamic Rotamer Libraries: Data-Driven Analysis of Side-Chain Conformational Propensities. PMID:26745530
The TIM Barrel Architecture Facilitated the Early Evolution of Protein-Mediated Metabolism. PMID:26733481
Recognition of a pseudo-symmetric RNA tetranucleotide by Csx3, a new member of the CRISPR associated Rossmann fold superfamily. PMID:26727591
An updated version of NPIDB includes new classifications of DNA-protein complexes and their families. PMID:26656949
MSAIndelFR: a scheme for multiple protein sequence alignment using information on indel flanking regions. PMID:26597571
KMAD: knowledge-based multiple sequence alignment for intrinsically disordered proteins. PMID:26568635
An assessment of catalytic residue 3D ensembles for the prediction of enzyme function. PMID:26538500
Clustering and percolation in protein loop structures. PMID:26510704
PDB-Explorer: a web-based interactive map of the protein data bank in shape space. PMID:26493835
Sequence and Structure Analysis of Distantly-Related Viruses Reveals Extensive Gene Transfer between Viruses and Hosts and among Viruses. PMID:26492264
BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology. PMID:26481362
The language of the protein universe. PMID:26451980
Diversity in protein domain superfamilies. PMID:26451979
Biogenesis and Homeostasis of Nicotinamide Adenine Dinucleotide Cofactor. PMID:26443758
SFESA: a web server for pairwise alignment refinement by secondary structure shifts. PMID:26335387
The value of protein structure classification information-Surveying the scientific literature. PMID:26313554
The history of the CATH structural classification of protein domains. PMID:26253692
Modularity of Protein Folds as a Tool for Template-Free Modeling of Structures. PMID:26252221
Critical evaluation of in silico methods for prediction of coiled-coil domains in proteins. PMID:26177815
Using homology relations within a database markedly boosts protein sequence similarity search. PMID:26038555
Protomers of protein hetero-oligomers tend to resemble each other more than expected. PMID:26034682
A large-scale structural classification of antimicrobial peptides. PMID:26000295
Function-selective domain architecture plasticity potentials in eukaryotic genome evolution. PMID:25980317
Functionally Structured Genomes in Lactobacillus kunkeei Colonizing the Honey Crop and Food Products of Honeybees and Stingless Bees. PMID:25953738
novPTMenzy: a database for enzymes involved in novel post-translational modifications. PMID:25931459
Routine phasing of coiled-coil protein crystal structures with AMPLE. PMID:25866657
Computational tools for epitope vaccine design and evaluation. PMID:25837467
Probing the protein interaction network of Pseudomonas aeruginosa cells by chemical cross-linking mass spectrometry. PMID:25800553
Application of data mining tools for classification of protein structural class from residue based averaged NMR chemical shifts. PMID:25758094
Aldolase as a chirality intersection of L-amino acids and D-sugars. PMID:25716920
Alteration of substrate specificity of alanine dehydrogenase. PMID:25538307
A hybrid method for identification of structural domains. PMID:25503992
Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. PMID:25503938
Achievements and challenges in structural bioinformatics and computational biophysics. PMID:25488929
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. PMID:25428375
The InterPro protein families database: the classification resource after 15 years. PMID:25428371
CFam: a chemical families database based on iterative selection of functional seeds and seed-directed compound clustering. PMID:25414339
PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs. PMID:25404129
Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions. PMID:25392414
dcGOR: an R package for analysing ontologies and protein domain annotations. PMID:25356683
The Comparative Genomics and Phylogenomics of Leishmania amazonensis Parasite. PMID:25336895
Bayesian model of protein primary sequence for secondary structure prediction. PMID:25314659
Molecular annotation of ketol-acid reductoisomerases from Streptomyces reveals a novel amino acid biosynthesis interlock mediated by enzyme promiscuity. PMID:25296650
Structural and functional characterization of ybr137wp implicates its involvement in the targeting of tail-anchored proteins to membranes. PMID:25288638
The intrinsically disordered regions of the Drosophila melanogaster Hox protein ultrabithorax select interacting proteins based on partner topology. PMID:25286318
NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection. PMID:25262355
How a spatial arrangement of secondary structure elements is dispersed in the universe of protein folds. PMID:25243952
Proteome-wide subcellular topologies of E. coli polypeptides database (STEPdb). PMID:25210196
Urzymology: experimental access to a key transition in the appearance of enzymes. PMID:25210034
The structure of mouse cytomegalovirus m04 protein obtained from sparse NMR data reveals a conserved fold of the m02-m06 viral immune modulator family. PMID:25126960
Genome-wide search for eliminylating domains reveals novel function for BLES03-like proteins. PMID:25062915
Crystal structures of three representatives of a new Pfam family PF14869 (DUF4488) suggest they function in sugar binding/uptake. PMID:25044324
The natural history of ADP-ribosyltransferases and the ADP-ribosylation system. PMID:25027823
Archaea: the first domain of diversified life. PMID:24987307
Identification of promiscuous ene-reductase activity by mining structural databases using active site constellations. PMID:24954722
Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of glycoside hydrolase. PMID:24938123
Cyanuric acid hydrolase from Azorhizobium caulinodans ORS 571: crystal structure and insights into a new class of Ser-Lys dyad proteins. PMID:24915109
Plant, animal, and fungal micronutrient queuosine is salvaged by members of the DUF2419 protein family. PMID:24911101
PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins. PMID:24857970
Dynamic programming used to align protein structures with a spectrum is robust. PMID:24833226
SymD webserver: a platform for detecting internally symmetric protein structures. PMID:24799435
Classification of intrinsically disordered regions and proteins. PMID:24773235
The origins of cellular life. PMID:24756907
The ensemble nature of allostery. PMID:24740064
Intermolecular β-strand networks avoid hub residues and favor low interconnectedness: a potential protection mechanism against chain dissociation upon mutation. PMID:24733378
Lactate racemase is a nickel-dependent enzyme activated by a widespread maturation system. PMID:24710389
Evolution and quantitative comparison of genome-wide protein domain distributions. PMID:24710298
Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms. PMID:24710297
The evolution of protein structures and structural ensembles under functional constraint. PMID:24710290
Reassessing domain architecture evolution of metazoan proteins: major impact of gene prediction errors. PMID:24710207
Systematic detection of internal symmetry in proteins using CE-Symm. PMID:24681267
Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis. PMID:24646163
A preliminary X-ray study of murine Tnfaip8/Oxi-α. PMID:24637935
Genomics and bioinformatics resources for translational science in Rosaceae. PMID:24634697
Elucidating common structural features of human pathogenic variations using large-scale atomic-resolution protein networks. PMID:24599843
Genome-wide structural modelling of TCR-pMHC interactions. PMID:24564684
Automatic classification of protein structures using low-dimensional structure space mappings. PMID:24564500
Global patterns of protein domain gain and loss in superkingdoms. PMID:24499935
Energetic frustrations in protein folding at residue resolution: a homologous simulation study of Im9 proteins. PMID:24498176
The cleverSuite approach for protein characterization: predictions of structural properties, solubility, chaperone requirements and RNA-binding abilities. PMID:24493033
Comparative analysis of proteomes and functionomes provides insights into origins of cellular diversification. PMID:24492748
Non-redundant unique interface structures as templates for modeling protein interactions. PMID:24475173
Effective moment feature vectors for protein domain structures. PMID:24391828
New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily. PMID:24383880
Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins. PMID:24364385
RepeatsDB: a database of tandem repeat protein structures. PMID:24311564
New perspectives on the diversification of the RNA interference system: insights from comparative genomics and small RNA sequencing. PMID:24311560
SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures. PMID:24304899
SCOP2 prototype: a new approach to protein structure mining. PMID:24293656
PDBe: Protein Data Bank in Europe. PMID:24288376
Revisiting amino acid substitution matrices for identifying distantly related proteins. PMID:24281694
The Structure-Function Linkage Database. PMID:24271399
Towards human-computer synergetic analysis of large-scale biological data. PMID:24267485
Classification of α-helical membrane proteins using predicted helix architectures. PMID:24204844
Elementary flux modes analysis of functional domain networks allows a better metabolic pathway interpretation. PMID:24204596
Comprehensive repertoire of foldable regions within whole genomes. PMID:24204229
An estimated 5% of new protein structures solved today represent a new Pfam family. PMID:24189229
Structure-based barcoding of proteins. PMID:24170674
On the role of aggregation prone regions in protein evolution, stability, and enzymatic catalysis: insights from diverse analyses. PMID:24146608
Defining structural and evolutionary modules in proteins: a community detection approach to explore sub-domain architecture. PMID:24131821
A horizontal alignment tool for numerical trend discovery in sequence data: application to protein hydropathy. PMID:24130469
Exploring mechanisms of human disease through structurally resolved protein interactome networks. PMID:24096645
Automatic identification of highly conserved family regions and relationships in genome wide datasets including remote protein sequences. PMID:24069417
Conformational flexibility of the leucine binding protein examined by protein domain coarse-grained molecular dynamics. PMID:24048570
Aminoacylation of tRNA 2'- or 3'-hydroxyl by phosphoseryl- and pyrrolysyl-tRNA synthetases. PMID:24021645
Novel autoproteolytic and DNA-damage sensing components in the bacterial SOS response and oxidized methylcytosine-induced eukaryotic DNA demethylation systems. PMID:23945014
One contact for every twelve residues allows robust and accurate topology-level protein structure modeling. PMID:23900763
PepBind: a comprehensive database and computational tool for analysis of protein-peptide interactions. PMID:23896518
Evolution of cytochrome bc complexes: from membrane-anchored dehydrogenases of ancient bacteria to triggers of apoptosis in vertebrates. PMID:23871937
A daily-updated tree of (sequenced) life as a reference for genome research. PMID:23778980
Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. PMID:23768067
Characterizing protein domain associations by Small-molecule ligand binding. PMID:23745168
IS-Dom: a dataset of independent structural domains automatically delineated from protein structures. PMID:23715893
Modeling proteins using a super-secondary structure library and NMR chemical shift information. PMID:23685209
CLCAs - a family of metalloproteases of intriguing phylogenetic distribution and with cases of substituted catalytic sites. PMID:23671590
EvoDesign: De novo protein design based on structural and evolutionary profiles. PMID:23671331
The wooly mutation (wly) on mouse chromosome 11 is associated with a genetic defect in Fam83g. PMID:23656696
The role of structural bioinformatics resources in the era of integrative structural biology. PMID:23633580
Crystal structure of the protein from Arabidopsis thaliana gene At5g06450, a putative DnaQ-like exonuclease domain-containing protein with homohexameric assembly. PMID:23616405
The challenge of increasing Pfam coverage of the human proteome. PMID:23603847
Understanding the folding-function tradeoff in proteins. PMID:23593437
Structure and function of the DUF2233 domain in bacteria and in the human mannose 6-phosphate uncovering enzyme. PMID:23572527
Rampant exchange of the structure and function of extramembrane domains between membrane and water soluble proteins. PMID:23555228
Viral evolution: Primordial cellular origins and late adaptation to parasitism. PMID:23550145
Two Fe-S clusters catalyze sulfur insertion by radical-SAM methylthiotransferases. PMID:23542644
Structure prediction and analysis of DNA transposon and LINE retrotransposon proteins. PMID:23530042
A domain-centric solution to functional genomics via dcGO Predictor. PMID:23514627
Functional site plasticity in domain superfamilies. PMID:23499848
Hierarchical classification of protein folds using a novel ensemble classifier. PMID:23437146
Predicting the binding patterns of hub proteins: a study using yeast protein interaction networks. PMID:23431393
Mining tertiary structural motifs for assessment of designability. PMID:23422424
Pseudomonas aeruginosa PA1006 is a persulfide-modified protein that is critical for molybdenum homeostasis. PMID:23409003
The repertoires of ubiquitinating and deubiquitinating enzymes in eukaryotic genomes. PMID:23393154
Evolutionary history of the TBP-domain superfamily. PMID:23376926
Evolutionary optimization of protein folding. PMID:23341762
Molecular modeling comparison of the performance of NS5b polymerase inhibitor (PSI-7977) on prevalent HCV genotypes. PMID:23322006
A dynamic data-driven framework for biological data using 2D barcodes. PMID:23304237
Structure-based redesign of proteins for minimal T-cell epitope content. PMID:23299435
Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets. PMID:23281852
In vivo translation rates can substantially delay the cotranslational folding of the Escherichia coli cytosolic proteome. PMID:23256155
TnpPred: A Web Service for the Robust Prediction of Prokaryotic Transposases. PMID:23251097
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. PMID:23203986
New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures. PMID:23203873
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. PMID:23203869
H-InvDB in 2013: an omics study platform for human functional gene and transcript discovery. PMID:23197657
LUCApedia: a database for the study of ancient life. PMID:23193296
NPIDB: Nucleic acid-Protein Interaction DataBase. PMID:23193292
Molecular evolution of translin superfamily proteins within the genomes of eubacteria, archaea and eukaryotes. PMID:23188094
Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB. PMID:23180575
BCL::Score--knowledge based energy potentials for ranking protein models represented by idealized secondary structure elements. PMID:23173051
This Déjà vu feeling--analysis of multidomain protein evolution in eukaryotic genomes. PMID:23166479
eProS--a database and toolbox for investigating protein sequence-structure-function relationships through energy profiles. PMID:23161695
DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. PMID:23161684
MetalPDB: a database of metal sites in biological macromolecular structures. PMID:23155064
Effective inter-residue contact definitions for accurate protein fold recognition. PMID:23140471
When a domain is not a domain, and why it is important to properly filter proteins in databases: conflicting definitions and fold classification systems for structural domains make filtering of such databases imperative. PMID:23108912
Evolutionarily consistent families in SCOP: sequence, structure and function. PMID:23078280
Inferences from structural comparison: flexibility, secondary structure wobble and sequence alignment optimization. PMID:23046301
Prediction of protein domain boundaries from inverse covariances. PMID:22987736
A modular perspective of protein structures: application to fragment based loop modeling. PMID:22987351
Automatic classification of protein structures relying on similarities between alignments. PMID:22974051
Benefits of using molecular structure and abundance in phylogenomic analysis. PMID:22973296
The enzymatic and metabolic capabilities of early life. PMID:22970111
Selective constraint on human pre-mRNA splicing by protein structural properties. PMID:22936073
Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya. PMID:22920653
Biphasic patterns of diversification and the emergence of modules. PMID:22891076
Characterization of Danio rerio Mn2+-dependent ADP-ribose/CDP-alcohol diphosphatase, the structural prototype of the ADPRibase-Mn-like protein family. PMID:22848751
Identification of catalytic residues using a novel feature that integrates the microenvironment and geometrical location properties of residues. PMID:22829945
Bacterial GRAS domain proteins throw new light on gibberellic acid response mechanisms. PMID:22829623
Template-based protein structure modeling using the RaptorX web server. PMID:22814390
GFam: a platform for automatic annotation of gene families. PMID:22790981
HEMD: an integrated tool of human epigenetic enzymes and chemical modulators for therapeutics. PMID:22761927
Overcoming sequence misalignments with weighted structural superposition. PMID:22733542
A global characterization and identification of multifunctional enzymes. PMID:22723914
Detecting mutually exclusive interactions in protein-protein interaction maps. PMID:22715412
NMR structure of lipoprotein YxeF from Bacillus subtilis reveals a calycin fold and distant homology with the lipocalin Blc from Escherichia coli. PMID:22693626
PBSword: a web server for searching similar protein-protein binding sites. PMID:22689645
KD4v: Comprehensible Knowledge Discovery System for Missense Variant. PMID:22641855
A multi-faceted analysis of RutD reveals a novel family of α/β hydrolases. PMID:22641504
The use of evolutionary patterns in protein annotation. PMID:22633559
Different evolutionary modifications as a guide to rewire two-component systems. PMID:22586357
Retinoid-binding proteins: similar protein architectures bind similar ligands via completely different ways. PMID:22574224
Adventures in data citation: sorghum genome data exemplifies the new gold standard. PMID:22571506
Transmembrane helix: simple or complex. PMID:22564899
Mapping the Anopheles gambiae odorant binding protein 1 (AgamOBP1) using modeling techniques, site directed mutagenesis, circular dichroism and ligand binding assays. PMID:22564768
Clusters of ancestrally related genes that show paralogy in whole or in part are a major feature of the genomes of humans and other species. PMID:22563380
A new size-independent score for pairwise protein structure alignment and its application to structure classification and nucleic-acid binding prediction. PMID:22522696
MSV3d: database of human MisSense Variants mapped to 3D protein structure. PMID:22491796
Functional repertoire, molecular pathways and diseases associated with 3D domain swapping in the human proteome. PMID:22472218
Membrane topology and predicted RNA-binding function of the 'early responsive to dehydration (ERD4)' plant protein. PMID:22431979
Ribosomal history reveals origins of modern protein synthesis. PMID:22427882
Evolutionary inaccuracy of pairwise structural alignments. PMID:22399676
Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies. PMID:22396634
Oligomerization of the reversibly glycosylated polypeptide: its role during rice plant development and in the regulation of self-glycosylation. PMID:22367534
Pleiotropic roles of a ribosomal protein in Dictyostelium discoideum. PMID:22363460
Further evidence for the likely completeness of the library of solved single domain protein structures. PMID:22272723
Structural differences between soluble and membrane bound cytochrome P450s. PMID:22244217
The phylogenomic roots of modern biochemistry: origins of proteins, cofactors and protein biosynthesis. PMID:22210458
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. PMID:22198341
ccPDB: compilation and creation of data sets from Protein Data Bank. PMID:22139939
MetaBase--the wiki-database of biological databases. PMID:22139927
DOMMINO: a database of macromolecular interactions. PMID:22135305
PoSSuM: a database of similar protein-ligand binding and putative pockets. PMID:22135290
IndelFR: a database of indels in protein structures and their flanking regions. PMID:22127860
PASS2 version 4: an update to the database of structure-based sequence alignments of structural domain superfamilies. PMID:22123743
ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree. PMID:22121228
On universal common ancestry, sequence similarity, and phylogenetic structure: the sins of P-values and the virtues of Bayesian evidence. PMID:22114984
PDBe: Protein Data Bank in Europe. PMID:22110033
PSCDB: a database for protein structural change upon ligand binding. PMID:22080505
Divergence and convergence in enzyme evolution. PMID:22069324
IDEAL: Intrinsically Disordered proteins with Extensive Annotations and Literature. PMID:22067451
Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins. PMID:22024092
canSAR: an integrated cancer public translational research and drug discovery resource. PMID:22013161
Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site. PMID:21998155
Active-site remodelling in the bifunctional fructose-1,6-bisphosphate aldolase/phosphatase. PMID:21983965
Transient knockdown and overexpression reveal a developmental role for the zebrafish enosf1b gene. PMID:21943404
Defense islands in bacterial and archaeal genomes and prediction of novel defense systems. PMID:21908672
OPM database and PPM web server: resources for positioning of proteins in membranes. PMID:21890895
Structure-based functional inference of hypothetical proteins from Mycoplasma hyopneumoniae. PMID:21870198
Small cofactors may assist protein emergence from RNA world: clues from RNA-protein complexes. PMID:21789260
Calculation of pK(a) in proteins with the microenvironment modulated-screened coulomb potential. PMID:21748803
AlignHUSH: alignment of HMMs using structure and hydrophobicity information. PMID:21729312
New structural and functional contexts of the Dx[DN]xDG linear motif: insights into evolution of calcium-binding proteins. PMID:21720552
FFAS server: novel features and applications. PMID:21715387
Ortholog identification in the presence of domain architecture rearrangement. PMID:21712343
Binary classification of protein molecules into intrinsically disordered and ordered segments. PMID:21693062
The role of protein conformational fluctuations in allostery, function, and evolution. PMID:21684672
MarkUs: a server to navigate sequence-structure-function space. PMID:21672961
Internal organization of large protein families: relationship between the sequence, structure, and function-based clustering. PMID:21671455
Why not consider a spherical protein? Implications of backbone hydrogen bonding for protein structure and function. PMID:21655593
Structure collisions between interacting proteins. PMID:21655095
A network of SCOP hidden Markov models and its analysis. PMID:21635719
Structural insights on two hypothetical secretion chaperones from Xanthomonas axonopodis pv. citri. PMID:21626158
The proteomic complexity and rise of the primordial ancestor of diversified life. PMID:21612591
Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis. PMID:21605342
Biological insights from topology independent comparison of protein 3D structures. PMID:21596786
The eisosome core is composed of BAR domain proteins. PMID:21593205
Structural similarity and classification of protein interaction interfaces. PMID:21589874
Combinations of protein-chemical complex structures reveal new targets for established drugs. PMID:21573205
Charged residues at protein interaction interfaces: unexpected conservation and orchestrated divergence. PMID:21563227
Functional diversification of the RING finger and other binuclear treble clef domains in prokaryotes and the early evolution of the ubiquitin system. PMID:21547297
Metagenomics and the protein universe. PMID:21497084
Revisiting gap locations in amino acid sequence alignments and a proposal for a method to improve them by introducing solvent accessibility. PMID:21465562
The Protein Data Bank in Europe (PDBe): bringing structure to biology. PMID:21460450
Prp8, the pivotal protein of the spliceosomal catalytic center, evolved from a retroelement-encoded reverse transcriptase. PMID:21441348
Characterizing the existing and potential structural space of proteins by large-scale multiple loop permutations. PMID:21376059
Protein function prediction: towards integration of similarity metrics. PMID:21353529
A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems. PMID:21306995
GOSSIP: a method for fast and accurate global alignment of protein structures. PMID:21296751
The nature of protein domain evolution: shaping the interaction network. PMID:21286315
Genome-wide analysis of PDZ domain binding reveals inherent functional overlap within the PDZ interaction network. PMID:21283644
XANNpred: neural nets that predict the propensity of a protein to yield diffraction-quality crystals. PMID:21246630
The combined effects of amino acid substitutions and indels on the evolution of structure within protein families. PMID:21179197
TMPad: an integrated structural database for helix-packing folds in transmembrane proteins. PMID:21177659
Improved protein surface comparison and application to low-resolution protein structure data. PMID:21172052
An Integrated Database for Complex Protein Structure Modeling. PMID:21151784
Amino acid patterns around disulfide bonds. PMID:21151463
Protein structure determination by exhaustive search of Protein Data Bank derived databases. PMID:21098306
Proteome evolution and the metabolic origins of translation and cellular life. PMID:21082171
BISC: binary subcomplexes in proteins database. PMID:21081561
Generation of a consensus protein domain dictionary. PMID:21068000
SUPERFAMILY 1.75 including a domain-centric gene ontology method. PMID:21062816
PolyQ: a database describing the sequence and domain context of polyglutamine repeats in proteins. PMID:21059684
Effect of using suboptimal alignments in template-based protein structure prediction. PMID:21058297
SAHG, a comprehensive database of predicted structures of all human proteins. PMID:21051360
Protein folds and protein folding. PMID:21051320
PDBe: Protein Data Bank in Europe. PMID:21045060
The RCSB Protein Data Bank: redesigned web site and web services. PMID:21036868
Verification of alternative splicing variants based on domain integrity, truncation length and intrinsic protein disorder. PMID:20972208
Analysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases in silico docked to different inhibitors. PMID:20961427
Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15. PMID:20944217
New variants of known folds: do they bring new biology? PMID:20944215
Structural classification of proteins and structural genomics: new insights into protein folding and evolution. PMID:20944210
Pre-calculated protein structure alignments at the RCSB PDB website. PMID:20937596
BSDB: the biomolecule stretching database. PMID:20929872
DAnCER: disease-annotated chromatin epigenetics resource. PMID:20876685
Tryptophanyl-tRNA synthetase Urzyme: a model to recapitulate molecular evolution and investigate intramolecular complementation. PMID:20864539
Template-based protein structure modeling. PMID:20835794
A score of the ability of a three-dimensional protein model to retrieve its own sequence as a quantitative measure of its quality and appropriateness. PMID:20830209
Solution structure and function of YndB, an AHSA1 protein from Bacillus subtilis. PMID:20818668
Fast and accurate protein substructure searching with simulated annealing and GPUs. PMID:20813068
Objective sequence-based subfamily classifications of mouse homeodomains reflect their in vitro DNA-binding preferences. PMID:20705649
More than 1,001 problems with protein domain databases: transmembrane regions, signal peptides and the issue of sequence homology. PMID:20686689
Genomic repertoires of DNA-binding transcription factors across the tree of life. PMID:20675356
Issues in bioinformatics benchmarking: the case study of multiple sequence alignment. PMID:20639539
Insights into Protein Sequence and Structure-Derived Features Mediating 3D Domain Swapping Mechanism using Support Vector Machine Based Approach. PMID:20634983
PROFESS: a PROtein function, evolution, structure and sequence database. PMID:20624718
Automatic structure classification of small proteins using random forest. PMID:20594334
Origins and diversification of a complex signal transduction system in prokaryotes. PMID:20587806
Reconstruction of gene association network reveals a transmembrane protein required for adipogenesis and targeted by PPARγ. PMID:20552250
MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data. PMID:20542913
Protein interface conservation across structure space. PMID:20534496
Sub-AQUA: real-value quality assessment of protein structure models. PMID:20525730
dockYard--a repository to assist modeling of protein-protein docking. PMID:20524020
A quick guide to large-scale genomic data mining. PMID:20523745
Protein annotation and modelling servers at University College London. PMID:20507913
Novel peptide-mediated interactions derived from high-resolution 3-dimensional structures. PMID:20502673
Synthesis of 5-hydroxyectoine from ectoine: crystal structure of the non-heme iron(II) and 2-oxoglutarate-dependent dioxygenase EctD. PMID:20498719
Computational protein design: validation and possible relevance as a tool for homology searching and fold recognition. PMID:20463972
Dali server: conservation mapping in 3D. PMID:20457744
Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution. PMID:20433725
Structural characteristics of novel protein folds. PMID:20421995
The evolution and functional repertoire of translation proteins following the origin of life. PMID:20377891
Fructose 1,6-bisphosphate aldolase/phosphatase may be an ancestral gluconeogenic enzyme. PMID:20348906
FragKB: structural and literature annotation resource of conserved peptide fragments and residues. PMID:20305778
New statistical potential for quality assessment of protein models and a survey of energy functions. PMID:20226048
Genomics and bioinformatics resources for crop improvement. PMID:20208064
CytokineDB: a database collecting biological information. PMID:20198179
How significant is a protein structure similarity with TM-score = 0.5? PMID:20164152
Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins. PMID:20162627
Analysis of CASP8 targets, predictions and assessment methods. PMID:20157476
Efficient protein alignment algorithm for protein search. PMID:20122207
HORI: a web server to compute Higher Order Residue Interactions in protein structures. PMID:20122196
The quorum-quenching N-acyl homoserine lactone acylase PvdQ is an Ntn-hydrolase with an unusual substrate-binding pocket. PMID:20080736
From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase. PMID:20043185
Protein comparison at the domain architecture level. PMID:19958515
ACLAME: a CLAssification of Mobile genetic Elements, update 2010. PMID:19933762
GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains. PMID:19923231
Analysis of HSP90-related folds with MED-SuMo classification approach. PMID:19920922
The Pfam protein families database. PMID:19920124
Splitting statistical potentials into meaningful scoring functions: testing the prediction of near-native structures from decoy conformations. PMID:19917096
MeMotif: a database of linear motifs in alpha-helical transmembrane proteins. PMID:19910368
PTGL: a database for secondary structure-based protein topologies. PMID:19906706
Intrinsic structural disorder confers cellular viability on oncogenic fusion proteins. PMID:19888473
PepX: a structural database of non-redundant protein-peptide complexes. PMID:19880386
Mechanical strength of 17,134 model proteins and cysteine slipknots. PMID:19876372
PDBe: Protein Data Bank in Europe. PMID:19858099
Revisiting the myths of protein interior: studying proteins with mass-fractal hydrophobicity-fractal and polarizability-fractal dimensions. PMID:19834622
Significant speedup of database searches with HMMs by search space reduction with PSSM family models. PMID:19828575
Survey of large protein complexes in D. vulgaris reveals great structural diversity. PMID:19805340
The continuity of protein structure space is an intrinsic property of proteins. PMID:19805219
A novel bioinformatics strategy for function prediction of poorly-characterized protein genes obtained from metagenome analyses. PMID:19801558
ProDaMa: an open source Python library to generate protein structure datasets. PMID:19799773
Exploration of uncharted regions of the protein universe. PMID:19787035
HHsvm: fast and accurate classification of profile-profile matches identified by HHsearch. PMID:19773335
Exploring protein structural dissimilarity to facilitate structure classification. PMID:19765314
FIGfams: yet another set of protein families. PMID:19762480
A survey of integral alpha-helical membrane proteins. PMID:19760129
The Gene Wiki: community intelligence applied to human gene annotation. PMID:19755503
An energetic representation of protein architecture that is independent of primary and secondary structure. PMID:19720035
Model for eukaryotic tail-anchored protein binding based on the structure of Get3. PMID:19706470
On the origin of life in the zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth. PMID:19703275
Overlapping genes produce proteins with unusual sequence properties and offer insight into de novo protein creation. PMID:19640978
Relative stabilities of conserved and non-conserved structures in the OB-fold superfamily. PMID:19564956
An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell. PMID:19536198
Molecular mimicry in innate immunity: crystal structure of a bacterial TIR domain. PMID:19535337
Characterization of the wheat endosperm transfer cell-specific protein TaPR60. PMID:19513805
Structural and functional analysis of Campylobacter jejuni PseG: a udp-sugar hydrolase from the pseudaminic acid biosynthetic pathway. PMID:19483088
Discrete-continuous duality of protein structure space. PMID:19482467
Biophysical studies support a predicted superhelical structure with armadillo repeats for Ric-8. PMID:19472323
The SALAMI protein structure search server. PMID:19465380
Tableau-based protein substructure search using quadratic programming. PMID:19450287
COMPASS server for homology detection: improved statistical accuracy, speed and functionality. PMID:19435884
Vaccinia virus G8R protein: a structural ortholog of proliferating cell nuclear antigen (PCNA). PMID:19421403
ProSMoS server: a pattern-based search using interaction matrix representation of protein structures. PMID:19420061
Development of an accurate classification system of proteins into structured and unstructured regions that uncovers novel structural domains: its application to human transcription factors. PMID:19402914
Exploiting structural classifications for function prediction: towards a domain grammar for protein function. PMID:19398323
Nothing about protein structure classification makes sense except in the light of evolution. PMID:19394812
Systematic comparison of SCOP and CATH: a new gold standard for protein structure analysis. PMID:19374763
ModLink+: improving fold recognition by using protein-protein interactions. PMID:19357100
Deciphering peculiar protein-protein interacting modules in Deinococcus radiodurans. PMID:19356244
FINDSITE: a combined evolution/structure-based approach to protein function prediction. PMID:19324930
Structure similarity measure with penalty for close non-equivalent residues. PMID:19321733
Co-evolution of primordial membranes and membrane proteins. PMID:19303305
Lipocalin signaling controls unicellular tube development in the Caenorhabditis elegans excretory system. PMID:19269285
Investigation of atomic level patterns in protein--small ligand interactions. PMID:19221587
Comparison of molecular dynamics and superfamily spaces of protein domain deformation. PMID:19220918
TransCent: computational enzyme design by transferring active sites and considering constraints relevant for catalysis. PMID:19208235
Structural genomics is the largest contributor of novel structural leverage. PMID:19194785
Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 A resolution. PMID:19173316
KAGIANA: an excel-based tool for retrieving summary information on Arabidopsis genes. PMID:19043069
SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny. PMID:19036790
The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions. PMID:18987007
CDD: specific functional annotation with the Conserved Domain Database. PMID:18984618
Unraveling the biochemistry and provenance of pupylation: a prokaryotic analog of ubiquitination. PMID:18980670
Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution. PMID:18840284
A method for probabilistic mapping between protein structure and function taxonomies through cross training. PMID:18834528
JAIL: a structure-based interface library for macromolecules. PMID:18832369
Structure-guided comparative analysis of proteins: principles, tools, and applications for predicting function. PMID:18818720
A novel CHHC Zn-finger domain found in spliceosomal proteins and tRNA modifying enzymes. PMID:18703587
The effectiveness of position- and composition-specific gap costs for protein similarity searches. PMID:18586708
Sequence analysis of GerM and SpoVS, uncharacterized bacterial 'sporulation' proteins with widespread phylogenetic distribution. PMID:18562273
Prevalence of intrinsic disorder in the intracellular region of human single-pass type I proteins: the case of the notch ligand Delta-4. PMID:18435556
SCOP database in 2004: refinements integrate structure and sequence family data PubMed citations: 327.

327 articles citing: SCOP database in 2004: refinements integrate structure and sequence family data

What Is Parvalbumin for? PMID:35625584
The aqueous humor proteome is intrinsically disordered. PMID:35128080
Erythropoietin Interacts with Specific S100 Proteins. PMID:35053268
Characterization of a Secretory YML079-like Cupin Protein That Contributes to Sclerotinia sclerotiorum Pathogenicity. PMID:34946121
SCOPe: improvements to the structural classification of proteins - extended database to facilitate variant interpretation and machine learning. PMID:34850923
Using Recursive Feature Selection with Random Forest to Improve Protein Structural Class Prediction for Low-Similarity Sequences. PMID:34055035
Intrinsic Disorder in Tetratricopeptide Repeat Proteins. PMID:32466138
Domain-mediated interactions for protein subfamily identification. PMID:31937869
Dynamical comparison between Drosha and Dicer reveals functional motion similarities and dissimilarities. PMID:31821368
Evolutionary adaptation in fucosyllactose uptake systems supports bifidobacteria-infant symbiosis. PMID:31489370
DISPOT: a simple knowledge-based protein domain interaction statistical potential. PMID:31350874
Differential proteostatic regulation of insoluble and abundant proteins. PMID:30903148
Dynamics based clustering of globin family members. PMID:30513111
SCOPe: classification of large macromolecular structures in the structural classification of proteins-extended database. PMID:30500919
A homologous mapping method for three-dimensional reconstruction of protein networks reveals disease-associated mutations. PMID:29560828
Protein-protein interface hot spots prediction based on a hybrid feature selection strategy. PMID:29334889
Computational design of fully overlapping coding schemes for protein pairs and triplets. PMID:29158504
A proteome view of structural, functional, and taxonomic characteristics of major protein domain clusters. PMID:29079755
Global organization of a binding site network gives insight into evolution and structure-function relationships of proteins. PMID:28912495
Discovery and evolution of novel hemerythrin genes in annelid worms. PMID:28330441
A Staphylococcus aureus Proteome Overview: Shared and Specific Proteins and Protein Complexes from Representative Strains of All Three Clades. PMID:28248218
SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins - extended Database. PMID:27914894
Three-Dimensional Biologically Relevant Spectrum (BRS-3D): Shape Similarity Profile Based on PDB Ligands as Molecular Descriptors. PMID:27869685
Prediction of interacting proteins from homology-modeled complex structures using sequence and structure scores. PMID:27857563
The archiving and dissemination of biological structure data. PMID:27450113
Comparative Protein Structure Modeling Using MODELLER. PMID:27322406
G-LoSA: An efficient computational tool for local structure-centric biological studies and drug design. PMID:26813336
Vasohibins: new transglutaminase-like cysteine proteases possessing a non-canonical Cys-His-Ser catalytic triad. PMID:26794318
Extending Protein Domain Boundary Predictors to Detect Discontinuous Domains. PMID:26502173
Temporal Gene Expression Profiles of Pre Blood-Fed Adult Females Immediately Following Eclosion in the Southern House Mosquito Culex Quinquefasciatus. PMID:26435696
The value of protein structure classification information-Surveying the scientific literature. PMID:26313554
X-ray Structural and Functional Studies of the Three Tandemly Linked Domains of Non-structural Protein 3 (nsp3) from Murine Hepatitis Virus Reveal Conserved Functions. PMID:26296883
Partial protein domains: evolutionary insights and bioinformatics challenges. PMID:25986583
Protein remote homology detection by combining Chou's distance-pair pseudo amino acid composition and principal component analysis. PMID:25896721
GS-align for glycan structure alignment and similarity measurement. PMID:25857669
Algorithmic approaches to protein-protein interaction site prediction. PMID:25713596
Genome sequence of Coxiella burnetii strain Namibia. PMID:25593636
INTEGRATING COMPUTATIONAL PROTEIN FUNCTION PREDICTION INTO DRUG DISCOVERY INITIATIVES. PMID:25530654
Protein structure annotation resources. PMID:25502191
Bayesian model of protein primary sequence for secondary structure prediction. PMID:25314659
The Protein Data Bank archive as an open data resource. PMID:25062767
Cross-species gene-family fluctuations reveal the dynamics of horizontal transfers. PMID:24829449
Redefining the PF06864 Pfam family based on Burkholderia pseudomallei PilO2(Bp) S-SAD crystal structure. PMID:24728008
Assessment of fully automated antibody homology modeling protocols in molecular operating environment. PMID:24715627
Improving protein function prediction using domain and protein complexes in PPI networks. PMID:24655481
Using distances between Top-n-gram and residue pairs for protein remote homology detection. PMID:24564580
The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification. PMID:24464998
ArchDB 2014: structural classification of loops in proteins. PMID:24265221
PAIRpred: partner-specific prediction of interacting residues from sequence and structure. PMID:24243399
Rebelling for a reason: protein structural "outliers". PMID:24073209
Protein similarity networks reveal relationships among sequence, structure, and function within the Cupin superfamily. PMID:24040257
Mechanisms of protein sequence divergence and incompatibility. PMID:23935519
A method for WD40 repeat detection and secondary structure prediction. PMID:23776530
PTS phosphorylation of Mga modulates regulon expression and virulence in the group A streptococcus. PMID:23651410
Comparison study on statistical features of predicted secondary structures for protein structural class prediction: From content to position. PMID:23641706
Structural and functional studies of S-adenosyl-L-methionine binding proteins: a ligand-centric approach. PMID:23617634
ProtoNet: charting the expanding universe of protein sequences. PMID:23563419
Concomitant prediction of function and fold at the domain level with GO-based profiles. PMID:23514233
Functional inference by ProtoNet family tree: the uncharacterized proteome of Daphnia pulex. PMID:23514195
Predicting the binding patterns of hub proteins: a study using yeast protein interaction networks. PMID:23431393
Toward a "structural BLAST": using structural relationships to infer function. PMID:23349097
Molecular modeling comparison of the performance of NS5b polymerase inhibitor (PSI-7977) on prevalent HCV genotypes. PMID:23322006
D²P²: database of disordered protein predictions. PMID:23203878
KIDFamMap: a database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms. PMID:23193279
2-nitrobenzoate 2-nitroreductase (NbaA) switches its substrate specificity from 2-nitrobenzoic acid to 2,4-dinitrobenzoic acid under oxidizing conditions. PMID:23123905
When a domain is not a domain, and why it is important to properly filter proteins in databases: conflicting definitions and fold classification systems for structural domains make filtering of such databases imperative. PMID:23108912
Evolutionarily consistent families in SCOP: sequence, structure and function. PMID:23078280
Meta-analysis of general bacterial subclades in whole-genome phylogenies using tree topology profiling. PMID:22915837
MoNetFamily: a web server to infer homologous modules and module-module interaction networks in vertebrates. PMID:22689643
Exploring protein dynamics space: the dynasome as the missing link between protein structure and function. PMID:22606222
Clusters of ancestrally related genes that show paralogy in whole or in part are a major feature of the genomes of humans and other species. PMID:22563380
A comparative analysis of protein targets of withdrawn cardiovascular drugs in human and mouse. PMID:22548699
Core site-moiety maps reveal inhibitors and binding mechanisms of orthologous proteins by screening compound libraries. PMID:22393385
Data ontology and an information system realization for web-based management of image measurements. PMID:22275893
Further evidence for the likely completeness of the library of solved single domain protein structures. PMID:22272723
Partner-aware prediction of interacting residues in protein-protein complexes from sequence data. PMID:22194998
InterEvol database: exploring the structure and evolution of protein complex interfaces. PMID:22053089
Independent subtilases expansions in fungi associated with animals. PMID:21727238
Difference in the distribution pattern of substrate enzymes in the metabolic network of Escherichia coli, according to chaperonin requirement. PMID:21702926
Structure-based prediction reveals capping motifs that inhibit β-helix aggregation. PMID:21685332
Why not consider a spherical protein? Implications of backbone hydrogen bonding for protein structure and function. PMID:21655593
Lateral transfer of genes and gene fragments in Staphylococcus extends beyond mobile elements. PMID:21622749
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. PMID:21472436
Touring protein space with Matt. PMID:21464511
A discriminative method for family-based protein remote homology detection that combines inductive logic programming and propositional models. PMID:21429187
Outer membrane proteins can be simply identified using secondary structure element alignment. PMID:21414186
Blurring contact maps of thousands of proteins: what we can learn by reconstructing 3D structure. PMID:21232136
Amino acid patterns around disulfide bonds. PMID:21151463
3D-interologs: an evolution database of physical protein- protein interactions across multiple genomes. PMID:21143789
SUPERFAMILY 1.75 including a domain-centric gene ontology method. PMID:21062816
Correlation to protein conformation of Wide-angle X-ray Scatter parameters. PMID:21046443
Conformational changes associated with the binding of zinc acetate at the putative active site of XcTcmJ, a cupin from Xanthomonas campestris pv. campestris. PMID:20944231
Structure of Bacteroides thetaiotaomicron BT2081 at 2.05 Å resolution: the first structural representative of a new protein family that may play a role in carbohydrate metabolism. PMID:20944224
A conserved fold for fimbrial components revealed by the crystal structure of a putative fimbrial assembly protein (BT1062) from Bacteroides thetaiotaomicron at 2.2 Å resolution. PMID:20944223
Structure of an essential bacterial protein YeaZ (TM0874) from Thermotoga maritima at 2.5 Å resolution. PMID:20944216
Molecular characterization, structural analysis and determination of host range of a novel bacteriophage LSB-1. PMID:20875143
CMASA: an accurate algorithm for detecting local protein structural similarity and its application to enzyme catalytic site annotation. PMID:20796320
Systematic analysis of short internal indels and their impact on protein folding. PMID:20684774
Understanding the effect of secondary structures and aggregation on human protein folding class evolution. PMID:20614111
Automatic structure classification of small proteins using random forest. PMID:20594334
The bridge-region of the Ku superfamily is an atypical zinc ribbon domain. PMID:20580930
dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment. PMID:20529369
PCFamily: a web server for searching homologous protein complexes. PMID:20511590
Computational protein design: validation and possible relevance as a tool for homology searching and fold recognition. PMID:20463972
Quantitative global studies of reactomes and metabolomes using a vectorial representation of reactions and chemical compounds. PMID:20406431
Protein sequences classification by means of feature extraction with substitution matrices. PMID:20377887
Mining Cytochrome b561 proteins from plant genomes. PMID:20223741
Characterization of protein secondary structure from NMR chemical shifts. PMID:20160946
Protein interactions and ligand binding: from protein subfamilies to functional specificity. PMID:20133844
Efficient protein alignment algorithm for protein search. PMID:20122207
Biana: a software framework for compiling biological interactions and analyzing networks. PMID:20105306
Conformational transitions upon ligand binding: holo-structure prediction from apo conformations. PMID:20066034
DescFold: a web server for protein fold recognition. PMID:20003426
Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences. PMID:20003388
A modular kernel approach for integrative analysis of protein domain boundaries. PMID:19958485
An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations. PMID:19851441
The continuity of protein structure space is an intrinsic property of proteins. PMID:19805219
Structural relationships among proteins with different global topologies and their implications for function annotation strategies. PMID:19805138
Structural snapshots of heparin depolymerization by heparin lyase I. PMID:19801541
FIGfams: yet another set of protein families. PMID:19762480
Enhanced protein fold recognition through a novel data integration approach. PMID:19709406
PDA: an automatic and comprehensive analysis program for protein-DNA complex structures. PMID:19594872
Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development. PMID:19543979
The SALAMI protein structure search server. PMID:19465380
Public databases and software for the pathway analysis of cancer genomes. PMID:19455256
PIRSF family classification system for protein functional and evolutionary analysis. PMID:19455212
PPISearch: a web server for searching homologous protein-protein interactions across multiple species. PMID:19417070
Genome-wide detection of hybrid genes with multiple components in human. PMID:19416550
Structure of Debaryomyces castellii CBS 2923 phytase. PMID:19342770
Biological sequences as pictures: a generic two dimensional solution for iterated maps. PMID:19335894
Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts. PMID:19289446
A feature-based approach to modeling protein-protein interaction hot spots. PMID:19273533
Are protein domains modules of lateral genetic transfer? PMID:19229333
Ab initio and template-based prediction of multi-class distance maps by two-dimensional recursive neural networks. PMID:19183478
Prediction of protein-protein interaction types using association rule based classification. PMID:19173748
Protein structure homology modeling using SWISS-MODEL workspace. PMID:19131951
Phylogenetic distribution and membrane topology of the LytR-CpsA-Psr protein family. PMID:19099556
Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks. PMID:19074493
Structural descriptor database: a new tool for sequence-based functional site prediction. PMID:19032768
Genome and proteome annotation: organization, interpretation and integration. PMID:19019817
Cavities and atomic packing in protein structures and interfaces. PMID:19005575
Prediction of protein structural classes using hybrid properties. PMID:18953662
The Bet v 1 fold: an ancient, versatile scaffold for binding of large, hydrophobic ligands. PMID:18922149
Structure of the cyclomodulin Cif from pathogenic Escherichia coli. PMID:18845161
Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations. PMID:18844985
SuperSite: dictionary of metabolite and drug binding sites in proteins. PMID:18842629
A method for probabilistic mapping between protein structure and function taxonomies through cross training. PMID:18834528
How well can the accuracy of comparative protein structure models be predicted? PMID:18832340
The unfoldomics decade: an update on intrinsically disordered proteins. PMID:18831774
Protein meta-functional signatures from combining sequence, structure, evolution, and amino acid property information. PMID:18818722
Comparison study on k-word statistical measures for protein: from sequence to 'sequence space'. PMID:18811946
Protein structure search and local structure characterization. PMID:18721472
Classifying RNA-binding proteins based on electrostatic properties. PMID:18716674
Ruffling of metalloporphyrins bound to IsdG and IsdI, two heme-degrading enzymes in Staphylococcus aureus. PMID:18713745
The cadherin superfamily in Anopheles gambiae: a comparative study with Drosophila melanogaster. PMID:18629193
Comprehensive 3D-modeling of allergenic proteins and amino acid composition of potential conformational IgE epitopes. PMID:18621419
Protein contact order prediction from primary sequences. PMID:18513429
SCPRED: accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences. PMID:18452616
Comparative protein structure modeling using Modeller. PMID:18428767
ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts. PMID:18325116
Improved general regression network for protein domain boundary prediction. PMID:18315843
Protein abundance profiling of the Escherichia coli cytosol. PMID:18304323
On the evolutionary significance and metal-binding characteristics of a monolobal transferrin from Ciona intestinalis. PMID:18287008
The origin of a novel gene through overprinting in Escherichia coli. PMID:18226237
In silico characterization of proteins: UniProt, InterPro and Integr8. PMID:18219596
A dynamic Bayesian network approach to protein secondary structure prediction. PMID:18218144
Preservation of protein clefts in comparative models. PMID:18199319
Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models? PMID:18179702
Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation. PMID:18158303
Function, structure, and evolution of the RubisCO-like proteins and their RubisCO homologs. PMID:18063718
Alternative splicing and protein structure evolution. PMID:18055499
Probing protein fold space with a simplified model. PMID:18054792
Framework for a protein ontology. PMID:18047702
The Pfam protein families database. PMID:18039703
Sequence-similar, structure-dissimilar protein pairs in the PDB. PMID:18004789
Data growth and its impact on the SCOP database: new developments. PMID:18000004
Improving model construction of profile HMMs for remote homology detection through structural alignment. PMID:17999748
Crystal structure of PhnH: an essential component of carbon-phosphorus lyase in Escherichia coli. PMID:17993513
MEROPS: the peptidase database. PMID:17991683
Metals in the "omics" world: copper homeostasis and cytochrome c oxidase assembly in a new light. PMID:17987327
PairsDB atlas of protein sequence space. PMID:17986464
ProCKSI: a decision support system for Protein (structure) Comparison, Knowledge, Similarity and Information. PMID:17963510
Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing. PMID:17941985
ProSAS: a database for analyzing alternative splicing in the context of protein structures. PMID:17933774
AutoPSI: a database for automatic structural classification of protein sequences and structures. PMID:17932066
Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world. PMID:17908824
Optimization of linear disorder predictors yields tight association between crystallographic disorder and hydrophobicity. PMID:17893360
MALISAM: a database of structurally analogous motifs in proteins. PMID:17855399
Distribution patterns of small-molecule ligands in the protein universe and implications for origin of life and drug discovery. PMID:17727706
Design of multi-specificity in protein interfaces. PMID:17722975
Multiple domain insertions and losses in the evolution of the Rab prenylation complex. PMID:17705859
Three-dimensional structure and ligand binding properties of trichosurin, a metatherian lipocalin from the milk whey of the common brushtail possum Trichosurus vulpecula. PMID:17685895
Comparative analysis of protein structure alignments. PMID:17672887
Applying negative rule mining to improve genome annotation. PMID:17659089
Natively unstructured loops differ from other loops. PMID:17658943
Evolution of function in the "two dinucleotide binding domains" flavoproteins. PMID:17658942
Bayesian refinement of protein functional site matching. PMID:17640336
NADP(H) phosphatase activities of archaeal inositol monophosphatase and eubacterial 3'-phosphoadenosine 5'-phosphate phosphatase. PMID:17616624
A topological algorithm for identification of structural domains of proteins. PMID:17608939
The role of hydrophobic interactions in positioning of peripheral proteins in membranes. PMID:17603894
Defining functional distance using manifold embeddings of gene ontology annotations. PMID:17595300
The AnnoLite and AnnoLyze programs for comparative annotation of protein structures. PMID:17570147
DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities. PMID:17567620
Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution. PMID:17535793
ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ. PMID:17526514
A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database. PMID:17521420
COMPASS server for remote homology inference. PMID:17517780
3D-partner: a web server to infer interacting partners and binding models. PMID:17517763
TAP score: torsion angle propensity normalization applied to local protein structure evaluation. PMID:17504537
fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies. PMID:17485476
DBAli tools: mining the protein structure space. PMID:17478513
Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners. PMID:17465672
In silico prediction of SARS protease inhibitors by virtual high throughput screening. PMID:17461975
A small cysteine-rich extracellular protein, VCRP, is inducible by the sex-inducer of Volvox carteri and by wounding. PMID:17431666
Evolution of protein complexes by duplication of homomeric interactions. PMID:17411433
Structural insight into repair of alkylated DNA by a new superfamily of DNA glycosylases comprising HEAT-like repeats. PMID:17395642
On the origin of the histone fold. PMID:17391511
The protein that binds to DNA base J in trypanosomatids has features of a thymidine hydroxylase. PMID:17389644
Topology of Type II REases revisited; structural classes and the common conserved core. PMID:17369272
Growth of novel protein structural data. PMID:17360626
Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint. PMID:17349043
Evaluation of the structural quality of modeled proteins by using globularity criteria. PMID:17346357
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases. PMID:17338813
Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database. PMID:17335583
FlowerPower: clustering proteins into domain architecture classes for phylogenomic inference of protein function. PMID:17288570
SCOOP: a simple method for identification of novel protein superfamily relationships. PMID:17277330
Characterization of a pseudomonad 2-nitrobenzoate nitroreductase and its catabolic pathway-associated 2-hydroxylaminobenzoate mutase and a chemoreceptor involved in 2-nitrobenzoate chemotaxis. PMID:17277060
Degradation of lambda-carrageenan by Pseudoalteromonas carrageenovora lambda-carrageenase: a new family of glycoside hydrolases unrelated to kappa- and iota-carrageenases. PMID:17269933
Improving the performance of DomainDiscovery of protein domain boundary assignment using inter-domain linker index. PMID:17254311
Using phylogeny to improve genome-wide distant homology recognition. PMID:17238281
A consensus view of protein dynamics. PMID:17215349
DiscoverySpace: an interactive data analysis application. PMID:17210078
A generalized analysis of hydrophobic and loop clusters within globular protein sequences. PMID:17210072
SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. PMID:17202171
Structure of a conserved hypothetical protein SA1388 from S. aureus reveals a capped hexameric toroid with two PII domain lids and a dinuclear metal center. PMID:17187687
Structure of ATP-bound human ATP:cobalamin adenosyltransferase. PMID:17176040
Protein Folding Database (PFD 2.0): an online environment for the International Foldeomics Consortium. PMID:17170010
Analysis of an optimal hidden Markov model for secondary structure prediction. PMID:17166267
Coverage of whole proteome by structural genomics observed through protein homology modeling database. PMID:17146617
A Protein Classification Benchmark collection for machine learning. PMID:17142240
The SUPERFAMILY database in 2007: families and functions. PMID:17098927
DWARF--a data warehouse system for analyzing protein families. PMID:17094801
PROTCOM: searchable database of protein complexes enhanced with domain-domain structures. PMID:17071962
Representing and comparing protein structures as paths in three-dimensional space. PMID:17052359
Interrogating the druggable genome with structural informatics. PMID:17031532
The many faces of protein-protein interactions: A compendium of interface geometry. PMID:17009862
The ancient Virus World and evolution of cells. PMID:16984643
Evolution of protein structural classes and protein sequence families. PMID:16959887
MultiSeq: unifying sequence and structure data for evolutionary analysis. PMID:16914055
Graemlin: general and robust alignment of multiple large interaction networks. PMID:16899655
A RecA-mediated exon profiling method. PMID:16896013
Protein structure database search and evolutionary classification. PMID:16885238
Improving the quality of protein structure models by selecting from alignment alternatives. PMID:16872519
The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains. PMID:16859499
AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. PMID:16855290
Crystal structure of a type III pantothenate kinase: insight into the mechanism of an essential coenzyme A biosynthetic enzyme universally distributed in bacteria. PMID:16855243
PreBI: prediction of biological interfaces of proteins in crystals. PMID:16844993
HHrep: de novo protein repeat detection and the origin of TIM barrels. PMID:16844977
Tools for integrated sequence-structure analysis with UCSF Chimera. PMID:16836757
Novel knowledge-based mean force potential at the profile level. PMID:16803615
Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties. PMID:16790052
A new measure for functional similarity of gene products based on Gene Ontology. PMID:16776819
A composite score for predicting errors in protein structure models. PMID:16751606
Automated functional classification of experimental and predicted protein structures. PMID:16749925
Statistical limits to the identification of ion channel domains by sequence similarity. PMID:16735758
Protein family expansions and biological complexity. PMID:16733546
Fold designability, distribution, and disease. PMID:16680196
Fold-recognition and comparative modeling of human alpha2,3-sialyltransferases reveal their sequence and structural similarities to CstII from Campylobacter jejuni. PMID:16620397
A tale of two ferredoxins: sequence similarity and structural differences. PMID:16603087
A comparative study of available software for high-accuracy homology modeling: from sequence alignments to structural models. PMID:16600967
Structural proteomics of minimal organisms: conservation of protein fold usage and evolutionary implications. PMID:16566839
Exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds. PMID:16549009
Strict rules determine arrangements of strands in sandwich proteins. PMID:16537492
The origins and evolution of functional modules: lessons from protein complexes. PMID:16524839
The proteome: structure, function and evolution. PMID:16524832
Exploiting protein structure data to explore the evolution of protein function and biological complexity. PMID:16524831
Hyaluronidases: their genomics, structures, and mechanisms of action. PMID:16522010
Mutations in the NB-ARC domain of I-2 that impair ATP hydrolysis cause autoactivation. PMID:16489136
Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space. PMID:16481312
Molecular analysis of receptor protein tyrosine phosphatase mu-mediated cell adhesion. PMID:16456543
Identification and characterization of RbmA, a novel protein required for the development of rugose colony morphology and biofilm structure in Vibrio cholerae. PMID:16428409
MaGe: a microbial genome annotation system supported by synteny results. PMID:16407324
The evolutionary relationship of the domain architectures in the RhoGEF-containing proteins. PMID:16393146
PUMA2--grid-based high-throughput analysis of genomes and metabolic pathways. PMID:16381888
The SWISS-MODEL Repository: new features and functionalities. PMID:16381875
SCOPPI: a structural classification of protein-protein interfaces. PMID:16381874
MODBASE: a database of annotated comparative protein structure models and associated resources. PMID:16381869
Gene3D: modelling protein structure, function and evolution. PMID:16381865
DMAPS: a database of multiple alignments for protein structures. PMID:16381863
Pfam: clans, web tools and services. PMID:16381856
MulPSSM: a database of multiple position-specific scoring matrices of protein domain families. PMID:16381855
LOCATE: a mouse protein subcellular localization database. PMID:16381849
IRESite: the database of experimentally verified IRES structures (www.iresite.org). PMID:16381829
The evolutionary history of Cys-tRNACys formation. PMID:16380427
Binding site-based classification of coronaviral papain-like proteases. PMID:16358325
Directed evolution of Streptomyces clavuligerus deacetoxycephalosporin C synthase for enhancement of penicillin G expansion. PMID:16332884
Evidence of a large novel gene pool associated with prokaryotic genomic islands. PMID:16299586
New genes from old: redeployment of dUTPase by herpesviruses. PMID:16188990
Dynamic covariation between gene expression and proteome characteristics. PMID:16131395
Functional annotation by identification of local surface similarities: a novel tool for structural genomics. PMID:16076399
MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences. PMID:16043635
Protein content of minimal and ancestral ribosome. PMID:16043494
Structure of a novel photoreceptor, the BLUF domain of AppA from Rhodobacter sphaeroides. PMID:15924418
Identification of genomic features using microsyntenies of domains: domain teams. PMID:15899966
Detecting remotely related proteins by their interactions and sequence similarity. PMID:15883372
The N-terminal to C-terminal motif in protein folding and function. PMID:15657118
3D models of yeast RNase P/MRP proteins Rpp1p and Pop3p. PMID:15613537
SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs. PMID:15608254
3did: interacting protein domains of known three-dimensional structure. PMID:15608228
The PEDANT genome database in 2005. PMID:15608204
PFD: a database for the investigation of protein folding kinetics and stability. PMID:15608196
E-MSD: an integrated data resource for bioinformatics. PMID:15608192
GenDiS: Genomic Distribution of protein structural domain Superfamilies. PMID:15608190
PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures. PMID:15608186
The ProDom database of protein domain families: more emphasis on 3D. PMID:15608179
InterPro, progress and status in 2005. PMID:15608177
ADDA: a domain database with global coverage of the protein universe. PMID:15608174
eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity. PMID:15608172
High-throughput computational and experimental techniques in structural genomics. PMID:15489337
Crystal structures of Escherichia coli ATP-dependent glucokinase and its complex with glucose. PMID:15466045
Structures of the Escherichia coli PutA proline dehydrogenase domain in complex with competitive inhibitors. PMID:15449943
The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases. PMID:15307895
SA-Search: a web tool for protein structure mining based on a Structural Alphabet. PMID:15215446
PRED-TMBB: a web server for predicting the topology of beta-barrel outer membrane proteins. PMID:15215419
Public web-based services from the European Bioinformatics Institute. PMID:15215339
Evidence for assembly of prions with left-handed beta-helices into trimers. PMID:15155909
Progress towards mapping the universe of protein folds. PMID:15128436
SCOP: a structural classification of proteins database PubMed citations: 153.

153 articles citing: SCOP: a structural classification of proteins database

Self-assembling peptides-based nano-cargos for targeted chemotherapy and immunotherapy of tumors: recent developments, challenges, and future perspectives. PMID:35403517
DBHR: a collection of databases relevant to human research. PMID:35251694
ProALIGN: Directly Learning Alignments for Protein Structure Prediction via Exploiting Context-Specific Alignment Motifs. PMID:35073170
Discovering the Ultimate Limits of Protein Secondary Structure Prediction. PMID:34827624
Topological and Structural Plasticity of the Single Ig Fold and the Double Ig Fold Present in CD19. PMID:34572502
Pretraining model for biological sequence data. PMID:34050350
BIO-GATS: A Tool for Automated GPCR Template Selection Through a Biophysical Approach for Homology Modeling. PMID:33898512
Development of a TSR-Based Method for Protein 3-D Structural Comparison With Its Applications to Protein Classification and Motif Discovery. PMID:33520934
The origin and evolution of viruses inferred from fold family structure. PMID:32748179
Prochlorococcus phage ferredoxin: structural characterization and electron transfer to cyanobacterial sulfite reductases. PMID:32434930
Self-analysis of repeat proteins reveals evolutionarily conserved patterns. PMID:32381046
Pseudo-Symmetric Assembly of Protodomains as a Common Denominator in the Evolution of Polytopic Helical Membrane Proteins. PMID:32189026
Similar genomic patterns of clinical infective endocarditis and oral isolates of Streptococcus sanguinis and Streptococcus gordonii. PMID:32066773
An Exploration of Common Greenhouse Gas Emissions by the Cyanobiont of the Azolla-Nostoc Symbiosis and Clues as to Nod Factors in Cyanobacteria. PMID:31835592
PDBe: improved findability of macromolecular structure data in the PDB. PMID:31691821
MANET 3.0: Hierarchy and modularity in evolving metabolic networks. PMID:31648227
CavBench: A benchmark for protein cavity detection methods. PMID:31609980
PDBe-KB: a community-driven resource for structural and functional annotations. PMID:31584092
Protodomains: Symmetry-Related Supersecondary Structures in Proteins and Self-Complementarity. PMID:30945220
Multi-criteria protein structure comparison and structural similarities analysis using pyMCPSC. PMID:30332415
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases. PMID:30084866
HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry. PMID:29846641
To what extent do structural changes in catalytic metal sites affect enzyme function? PMID:29161638
RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education. PMID:29067736
Systematic Mutagenesis of Serine Hydroxymethyltransferase Reveals an Essential Role in Nematode Resistance. PMID:28912378
Exploring general-purpose protein features for distinguishing enzymes and non-enzymes within the twilight zone. PMID:28732462
Structure, kinetic characterization and subcellular localization of the two ribulose 5-phosphate epimerase isoenzymes from Trypanosoma cruzi. PMID:28207833
pHMM-tree: phylogeny of profile hidden Markov models. PMID:28062446
Structure, Catalysis, and Inhibition of OfChi-h, the Lepidoptera-exclusive Insect Chitinase. PMID:28053084
Identification of internalin-A-like virulent proteins in Leishmania donovani. PMID:27765050
Sequence Analysis of Hypothetical Proteins from Helicobacter pylori 26695 to Identify Potential Virulence Factors. PMID:27729842
PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps. PMID:27710935
An efficient algorithm for protein structure comparison using elastic shape analysis. PMID:27708689
ORION: a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles. PMID:27319297
GenFamClust: an accurate, synteny-aware and reliable homology inference algorithm. PMID:27260514
CASP 11 target classification. PMID:26756794
Connectivity Homology Enables Inter-Species Network Models of Synthetic Lethality. PMID:26451775
The value of protein structure classification information-Surveying the scientific literature. PMID:26313554
Prediction of structural features and application to outer membrane protein identification. PMID:26104144
ChSeq: A database of chameleon sequences. PMID:25970262
Dynamics of equilibrium folding and unfolding transitions of titin immunoglobulin domain under constant forces. PMID:25726700
Evaluation and improvements of clustering algorithms for detecting remote homologous protein families. PMID:25651949
Novel mutations confirm that COL11A2 is responsible for autosomal recessive non-syndromic hearing loss DFNB53. PMID:25633957
Putative E3 ubiquitin ligase of human rotavirus inhibits NF-κB activation by using molecular mimicry to target β-TrCP. PMID:25626907
Comparative genomics of nucleotide metabolism: a tour to the past of the three cellular domains of life. PMID:25230797
A new statistical framework to assess structural alignment quality using information compression. PMID:25161241
Hamiltonian Switch Metropolis Monte Carlo Simulations for Improved Conformational Sampling of Intrinsically Disordered Regions Tethered to Ordered Domains of Proteins. PMID:25136274
Conserved evolutionary units in the heme-copper oxidase superfamily revealed by novel homologous protein families. PMID:24931479
Dynamic programming used to align protein structures with a spectrum is robust. PMID:24833226
Computational design of binding proteins to EGFR domain II. PMID:24710267
A method to predict edge strands in beta-sheets from protein sequences. PMID:24688737
De novo structure prediction of globular proteins aided by sequence variation-derived contacts. PMID:24637808
Exploring fold space preferences of new-born and ancient protein superfamilies. PMID:24244135
Rebelling for a reason: protein structural "outliers". PMID:24073209
kClust: fast and sensitive clustering of large protein sequence databases. PMID:23945046
Structure of the Chlamydia trachomatis immunodominant antigen Pgp3. PMID:23703617
DomHR: accurately identifying domain boundaries in proteins using a hinge region strategy. PMID:23593247
Functional inference by ProtoNet family tree: the uncharacterized proteome of Daphnia pulex. PMID:23514195
A conserved START domain coenzyme Q-binding polypeptide is required for efficient Q biosynthesis, respiratory electron transport, and antioxidant function in Saccharomyces cerevisiae. PMID:23270816
Describing sequence-ensemble relationships for intrinsically disordered proteins. PMID:23240611
Analysis of conformational variation in macromolecular structural models. PMID:22808083
How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis. PMID:22759650
Dengue virus nonstructural protein 5 adopts multiple conformations in solution. PMID:22757685
PocketAnnotate: towards site-based function annotation. PMID:22618878
DBETH: a Database of Bacterial Exotoxins for Human. PMID:22102573
SCOWLP update: 3D classification of protein-protein, -peptide, -saccharide and -nucleic acid interactions, and structure-based binding inferences across folds. PMID:21992011
Delineation of lipopolysaccharide (LPS)-binding sites on hemoglobin: from in silico predictions to biophysical characterization. PMID:21900232
Improving the prediction of protein binding sites by combining heterogeneous data and Voronoi diagrams. PMID:21861881
Protein sequence alignment with family-specific amino acid similarity matrices. PMID:21846354
PredUs: a web server for predicting protein interfaces using structural neighbors. PMID:21609948
Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites. PMID:21342566
A mathematical framework for protein structure comparison. PMID:21304929
Searching the protein structure database for ligand-binding site similarities using CPASS v.2. PMID:21269480
GOAPhAR: An Integrative Discovery Tool for Annotation, Pathway Analysis. PMID:21132056
FragmentStore--a comprehensive database of fragments linking metabolites, toxic molecules and drugs. PMID:20965964
Protein folding pathways and state transitions described by classical equations of motion of an elastic network model. PMID:20954241
Prototypes of elementary functional loops unravel evolutionary connections between protein functions. PMID:20823313
Hidden Markov model speed heuristic and iterative HMM search procedure. PMID:20718988
Structural conservation predominates over sequence variability in the crown of HIV type 1's V3 loop. PMID:20560796
SARS coronavirus unique domain: three-domain molecular architecture in solution and RNA binding. PMID:20493876
Characterization of protein secondary structure from NMR chemical shifts. PMID:20160946
Nuclear magnetic resonance structure of the nucleic acid-binding domain of severe acute respiratory syndrome coronavirus nonstructural protein 3. PMID:19828617
Evolutionary descent of prion genes from the ZIP family of metal ion transporters. PMID:19784368
Enhanced protein fold recognition through a novel data integration approach. PMID:19709406
Biological sequence simulation for testing complex evolutionary hypotheses: indel-Seq-Gen version 2.0. PMID:19651852
Crystal structure of the variable domain of the Streptococcus gordonii surface protein SspB. PMID:19609934
The GD box: a widespread noncontiguous supersecondary structural element. PMID:19609930
Efficient use of unlabeled data for protein sequence classification: a comparative study. PMID:19426450
Patterns of insertion and deletion in Mammalian genomes. PMID:19412437
Sm/Lsm genes provide a glimpse into the early evolution of the spliceosome. PMID:19282982
Predicting peptide structures in native proteins from physical simulations of fragments. PMID:19197352
An unusually small dimer interface is observed in all available crystal structures of cytosolic sulfotransferases. PMID:19173308
Structural analysis of linear and conformational epitopes of allergens. PMID:19121639
The protein structure initiative structural genomics knowledgebase. PMID:19010965
SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling. PMID:18989261
Tandem duplication, circular permutation, molecular adaptation: how Solanaceae resist pests via inhibitors. PMID:18315854
Universality and diversity of folding mechanics for three-helix bundle proteins. PMID:18195374
CancerLectinDB: a database of lectins relevant to cancer. PMID:18038206
Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PMID:17373854
Bioinformatics approaches to classifying allergens and predicting cross-reactivity. PMID:17276876
Divergent evolution of a structural proteome: phenomenological models. PMID:17071665
Functional classification using phylogenomic inference. PMID:16846248
Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet. PMID:16844973
Statistical limits to the identification of ion channel domains by sequence similarity. PMID:16735758
Statistics of knots, geometry of conformations, and evolution of proteins. PMID:16710448
The RCSB PDB information portal for structural genomics. PMID:16381872
Secondary structure assignment that accurately reflects physical and evolutionary characteristics. PMID:16351757
Structural evolution of the protein kinase-like superfamily. PMID:16244704
PALSSE: a program to delineate linear secondary structural elements from protein structures. PMID:16095538
The Cm56 tRNA modification in archaea is catalyzed either by a specific 2'-O-methylase, or a C/D sRNP. PMID:15987815
Assessing strategies for improved superfamily recognition. PMID:15937274
S4: structure-based sequence alignments of SCOP superfamilies. PMID:15608181
Automatic generation and evaluation of sparse protein signatures for families of protein structural domains. PMID:15608116
Amino acid signaling in yeast: casein kinase I and the Ssy5 endoprotease are key determinants of endoproteolytic activation of the membrane-bound Stp1 transcription factor. PMID:15509782
Estimates of statistical significance for comparison of individual positions in multiple sequence alignments. PMID:15296518
Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1. PMID:15287974
Network analysis of metabolic enzyme evolution in Escherichia coli. PMID:15113413
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PMID:15103394
The NMR solution structure of the 30S ribosomal protein S27e encoded in gene RS27_ARCFU of Archaeoglobus fulgidis reveals a novel protein fold. PMID:15096641
Structural basis of the interaction between the AAA ATPase p97/VCP and its adaptor protein p47. PMID:14988733
Evolutionary families of peptidase inhibitors. PMID:14705960
Detection of homologous proteins by an intermediate sequence search. PMID:14691221
Functional map and domain structure of MET, the product of the c-met protooncogene and receptor for hepatocyte growth factor/scatter factor. PMID:14528000
Finding evolutionary relations beyond superfamilies: fold-based superfamilies. PMID:14500881
Integrated mapping, chromosomal sequencing and sequence analysis of Cryptosporidium parvum. PMID:12869580
ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure. PMID:12824423
Detection of reliable and unexpected protein fold predictions using 3D-Jury. PMID:12824309
A novel member of the split betaalphabeta fold: Solution structure of the hypothetical protein YML108W from Saccharomyces cerevisiae. PMID:12717036
Bioinformatics methods to predict protein structure and function. A practical approach. PMID:12632698
Structural classification of zinc fingers: survey and summary. PMID:12527760
Transmembrane helix predictions revisited. PMID:12441377
Structural characterization of the human proteome. PMID:12421749
MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. PMID:12381844
The skeletal muscle Ca2+ release channel has an oxidoreductase-like domain. PMID:12218169
The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties. PMID:12186647
Comparison of the small molecule metabolic enzymes of Escherichia coli and Saccharomyces cerevisiae. PMID:12045145
Interrogating protein interaction networks through structural biology. PMID:11972061
An efficient algorithm for large-scale detection of protein families. PMID:11917018
Comparative genomics and evolution of proteins involved in RNA metabolism. PMID:11917006
Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database. PMID:11875040
Surviving in a sea of data: a survey of plant genome data resources and issues in building data management systems. PMID:11860214
Functional evolution of two subtly different (similar) folds. PMID:11782293
Exon structure conservation despite low sequence similarity: a relic of dramatic events in evolution? PMID:11574467
Comparing function and structure between entire proteomes. PMID:11567088
Functional versatility and molecular diversity of the metabolic map of Escherichia coli. PMID:11544193
The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases. PMID:11276424
Sialidase-like Asp-boxes: sequence-similar structures within different protein folds. PMID:11266614
KH domain: one motif, two folds. PMID:11160884
CKAAPs DB: a conserved key amino acid positions database. PMID:11125128
A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm. PMID:11125099
PALI-a database of Phylogeny and ALIgnment of homologous protein structures. PMID:11125050
SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. PMID:10982859
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. PMID:10802651
SCOP database in 2002: refinements accommodate structural genomics PubMed citations: 145.

145 articles citing: SCOP database in 2002: refinements accommodate structural genomics

SCOPe: improvements to the structural classification of proteins - extended database to facilitate variant interpretation and machine learning. PMID:34850923
SCOPe: classification of large macromolecular structures in the structural classification of proteins-extended database. PMID:30500919
Metabolic Pathway Assignment of Plant Genes based on Phylogenetic Profiling-A Feasibility Study. PMID:29163570
From malaria to cancer: Computational drug repositioning of amodiaquine using PLIP interaction patterns. PMID:28900272
Structure of the 40S ribosomal subunit of Plasmodium falciparum by homology and de novo modeling. PMID:28119814
SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins - extended Database. PMID:27914894
Three-Dimensional Biologically Relevant Spectrum (BRS-3D): Shape Similarity Profile Based on PDB Ligands as Molecular Descriptors. PMID:27869685
The value of protein structure classification information-Surveying the scientific literature. PMID:26313554
Customised fragments libraries for protein structure prediction based on structural class annotations. PMID:25925397
Rapid search for tertiary fragments reveals protein sequence-structure relationships. PMID:25420575
SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures. PMID:24304899
SCOP2 prototype: a new approach to protein structure mining. PMID:24293656
Protein similarity networks reveal relationships among sequence, structure, and function within the Cupin superfamily. PMID:24040257
Efficient protein structure search using indexing methods. PMID:23691543
The effect of edge definition of complex networks on protein structure identification. PMID:23533536
Molecular modeling comparison of the performance of NS5b polymerase inhibitor (PSI-7977) on prevalent HCV genotypes. PMID:23322006
A global comparison of the human and T. brucei degradomes gives insights about possible parasite drug targets. PMID:23236535
Genomic and functional characterization of the diverse immunoglobulin domain-containing protein (DICP) family. PMID:22386706
The dynamic determinants of reaction specificity in the IMPDH/GMPR family of (β/α)(8) barrel enzymes. PMID:22332716
Cofactor mobility determines reaction outcome in the IMPDH and GMPR (β-α)8 barrel enzymes. PMID:22037469
A network of SCOP hidden Markov models and its analysis. PMID:21635719
Evaluating the solution from MrBUMP and BALBES. PMID:21460449
BSDB: the biomolecule stretching database. PMID:20929872
Protein-protein docking benchmark version 4.0. PMID:20806234
Recognition of beta-structural motifs using hidden Markov models trained with simulated evolution. PMID:20529918
Efficient protein alignment algorithm for protein search. PMID:20122207
Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB). PMID:20066127
Conformational transitions upon ligand binding: holo-structure prediction from apo conformations. PMID:20066034
Mechanical strength of 17,134 model proteins and cysteine slipknots. PMID:19876372
The continuity of protein structure space is an intrinsic property of proteins. PMID:19805219
Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII. PMID:19729506
The SALAMI protein structure search server. PMID:19465380
Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures. PMID:19325884
Accurate prediction of peptide binding sites on protein surfaces. PMID:19325869
Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts. PMID:19289446
Prediction of protein structural classes using hybrid properties. PMID:18953662
Comprehensive 3D-modeling of allergenic proteins and amino acid composition of potential conformational IgE epitopes. PMID:18621419
Rapid comparison of properties on protein surface. PMID:18618695
Superimpose: a 3D structural superposition server. PMID:18492720
Overview of protein structural and functional folds. PMID:18429251
Interrogating domain-domain interactions with parsimony based approaches. PMID:18366803
MrBUMP: an automated pipeline for molecular replacement. PMID:18094475
Probing protein fold space with a simplified model. PMID:18054792
Data growth and its impact on the SCOP database: new developments. PMID:18000004
Synonymous codon usage in different protein secondary structural classes of human genes: implication for increased non-randomness of GC3 rich genes towards protein stability. PMID:17914237
Partially folded states of staphylococcal nuclease highlight the conserved structural hierarchy of OB-fold proteins. PMID:17661445
Malonyl-CoA: acyl carrier protein transacylase from Helicobacter pylori: Crystal structure and its interaction with acyl carrier protein. PMID:17525466
In silico prediction of SARS protease inhibitors by virtual high throughput screening. PMID:17461975
Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PMID:17373854
SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. PMID:17202171
Coverage of whole proteome by structural genomics observed through protein homology modeling database. PMID:17146617
A framework for protein structure classification and identification of novel protein structures. PMID:17042958
Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction. PMID:16970830
MANET: tracing evolution of protein architecture in metabolic networks. PMID:16854231
PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins. PMID:16844988
Identification of putative domain linkers by a neural network - application to a large sequence database. PMID:16800897
Statistical limits to the identification of ion channel domains by sequence similarity. PMID:16735758
From the similarity analysis of protein cavities to the functional classification of protein families using cavbase. PMID:16697007
A comparative study of available software for high-accuracy homology modeling: from sequence alignments to structural models. PMID:16600967
GNARE: automated system for high-throughput genome analysis with grid computational backend. PMID:16328950
Divergent evolution within protein superfolds inferred from profile-based phylogenetics. PMID:16266719
Solution Structure of MTH0776 from Methanobacterium thermoautotrophicum. PMID:16222557
Characterization of carbohydrate-binding cytochrome b562 from the white-rot fungus Phanerochaete chrysosporium. PMID:16085848
A sequence sub-sampling algorithm increases the power to detect distant homologues. PMID:16006623
ProTarget: automatic prediction of protein structure novelty. PMID:15980586
Universal sharing patterns in proteomes and evolution of protein fold architecture and life. PMID:15883883
Structural similarity to bridge sequence space: finding new families on the bridges. PMID:15840833
A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles. PMID:15819976
Practical lessons from protein structure prediction. PMID:15805122
Super paramagnetic clustering of protein sequences. PMID:15804359
Identification of the ligand binding sites on the molecular surface of proteins. PMID:15689509
Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method. PMID:15647112
Phylogeny determined by protein domain content. PMID:15630082
The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. PMID:15608185
Modeling the helicase domain of Brome mosaic virus 1a replicase. PMID:15597207
Components of coated vesicles and nuclear pore complexes share a common molecular architecture. PMID:15523559
PASBio: predicate-argument structures for event extraction in molecular biology. PMID:15494078
When proteome meets genome: the alpha helix and the beta strand of proteins are eschewed by mRNA splice junctions and may define the minimal indivisible modules of protein architecture. PMID:15381847
Single amino acid changes in AspRS reveal alternative routes for expanding its tRNA repertoire in vivo. PMID:15289581
Sequence-based prediction of protein domains. PMID:15240828
CHOP: parsing proteins into structural domains. PMID:15215452
The dependence of all-atom statistical potentials on structural training database. PMID:15189839
Solution structure of the hypothetical protein Mth677 from Methanobacterium thermoautotrophicum: a novel alpha+beta fold. PMID:15152082
Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. PMID:15140832
A Structural-informatics approach for tracing beta-sheets: building pseudo-C(alpha) traces for beta-strands in intermediate-resolution density maps. PMID:15123425
Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae. PMID:15121896
A hybrid clustering approach to recognition of protein families in 114 microbial genomes. PMID:15115543
Functional classification of proteins and protein variants. PMID:15087495
A Hidden Markov Model method, capable of predicting and discriminating beta-barrel outer membrane proteins. PMID:15070403
Structural characterization of genomes by large scale sequence-structure threading. PMID:15061866
The nonconserved wrapping of conserved protein folds reveals a trend toward increasing connectivity in proteomic networks. PMID:14978274
TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics. PMID:14724320
Evolutionary families of peptidase inhibitors. PMID:14705960
The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold. PMID:14687415
GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins. PMID:14681418
3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes. PMID:14681404
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models. PMID:14681401
SCOP database in 2004: refinements integrate structure and sequence family data. PMID:14681400
E-MSD: an integrated data resource for bioinformatics. PMID:14681397
HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database. PMID:14681395
DomIns: a web resource for domain insertions in known protein structures. PMID:14681392
The ASTRAL Compendium in 2004. PMID:14681391
EyeSite: a semi-automated database of protein families in the eye. PMID:14681381
ESTHER, the database of the alpha/beta-hydrolase fold superfamily of proteins. PMID:14681380
SMART 4.0: towards genomic data integration. PMID:14681379
The Pfam protein families database. PMID:14681378
PIRSF: family classification system at the Protein Information Resource. PMID:14681371
ACLAME: a CLAssification of Mobile genetic Elements. PMID:14681355
Phylogenomic identification of five new human homologs of the DNA repair enzyme AlkB. PMID:14667252
Characteristics and prediction of domain linker sequences in multi-domain proteins. PMID:14649291
Multi-domain protein families and domain pairs: comparison with known structures and a random model of domain recombination. PMID:14649290
Bioinformatics Resources for In Silico Proteome Analysis. PMID:14615630
Enzyme-specific profiles for genome annotation: PRIAM. PMID:14602924
ELISA: structure-function inferences based on statistically significant and evolutionarily inspired observations. PMID:12952559
A comparative proteomics resource: proteins of Arabidopsis thaliana. PMID:12914659
Structural details (kinks and non-alpha conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors. PMID:12888523
Identification of protein biochemical functions by similarity search using the molecular surface database eF-site. PMID:12876308
An evolutionarily structured universe of protein architecture. PMID:12840035
GlobPlot: Exploring protein sequences for globularity and disorder. PMID:12824398
Integrated databanks access and sequence/structure analysis services at the PBIL. PMID:12824334
MATRAS: A program for protein 3D structure comparison. PMID:12824329
NCI: A server to identify non-canonical interactions in protein structures. PMID:12824323
Cytokine-related genes identified from the RIKEN full-length mouse cDNA data set. PMID:12819128
Kinase pathway database: an integrated protein-kinase and NLP-based protein-interaction resource. PMID:12799355
A comparison of Pfam and MEROPS: two databases, one comprehensive, and one specialised. PMID:12740029
The structure of nonvertebrate actin: implications for the ATP hydrolytic mechanism. PMID:12732734
A network of rice genes associated with stress response and seed development. PMID:12684538
The structure of full-length LysR-type transcriptional regulators. Modeling of the full-length OxyR transcription factor dimer. PMID:12595552
Evolution of transcription factors and the gene regulatory network in Escherichia coli. PMID:12582243
Identification of a novel Bardet-Biedl syndrome protein, BBS7, that shares structural features with BBS1 and BBS2. PMID:12567324
Improving the performance of DomainParser for structural domain partition using neural network. PMID:12560490
Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases. PMID:12553882
Structural classification of zinc fingers: survey and summary. PMID:12527760
The Structure Superposition Database. PMID:12520064
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003. PMID:12520060
Gene3D: structural assignments for the biologist and bioinformaticist alike. PMID:12520054
Enlarged FAMSBASE: protein 3D structure models of genome sequences for 41 species. PMID:12520053
The Proteome Analysis database: a tool for the in silico analysis of whole proteomes. PMID:12520037
The InterPro Database, 2003 brings increased coverage and new features. PMID:12520011
The PEDANT genome database. PMID:12519983
Sputnik: a database platform for comparative plant genomics. PMID:12519965
Transmembrane helix predictions revisited. PMID:12441377
The PRC-barrel: a widespread, conserved domain shared by photosynthetic reaction center subunits and proteins of RNA metabolism. PMID:12429060
Human non-synonymous SNPs: server and survey. PMID:12202775
ASTRAL compendium enhancements. PMID:11752310