PDB_REDO databank

Names
More detailed information about this field from each metasource.

PDB_REDO databank
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:38.349519

pdb_redo
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:38.349519

Other names: pdb_redo

This source may no longer be available. No known URL could be resolved successfully.

The PDB_REDO databank contains alternative (in many cases higher quality) versions of Protein Data Bank (PDB) structure models that were optimised by model refinement and rebuilding. The structure models are supplemented by validation data that describe model quality and model changes with respect to the PDB version. As the models are consistently treated, they are more suited for large-scale analysis of protein structure than their PDB counterparts.

Webpage:

http://www.cmbi.ru.nl/pdb_redo

Publications: (9)

Publications
More detailed information about this field from each metasource.

A series of PDB related databases for everyday needs
PMID: 21071423
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:38.349519

A series of PDB-related databanks for everyday needs
PMID: 25352545
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:38.349519

PDB_REDO: automated re-refinement of X-ray structure models in the PDB
PMID: 22477769
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:38.349519

PDB_REDO: constructive validation, more than just looking for errors
PMID: 22505269
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:38.349519

Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank
PMID: 22034521
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:38.349519

Re-refinement from deposited X-ray data can deliver improved models for most PDB entries
PMID: 19171973
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:38.349519

PDB improvement starts with data deposition
PMID: 17626865
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:38.349519

Validation and correction of Zn-Cys x His y complexes
PMID: 27710932
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:38.349519

Data Mining of Macromolecular Structures
PMID: 27115630
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:38.349519

A series of PDB related databases for everyday needs PubMed citations: 249.

249 articles citing: A series of PDB related databases for everyday needs

Comprehensive Assessment of Indian Variations in the Druggable Kinome Landscape Highlights Distinct Insights at the Sequence, Structure and Pharmacogenomic Stratum. PMID:35865963
De novo design of discrete, stable 310-helix peptide assemblies. PMID:35732733
Characterization of mutations modulating enhanced transmissibility of SARS-CoV-2 B.1.617+ (Delta) variant using In Silico tools. PMID:35721780
The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature. PMID:35622909
LoopGrafter: a web tool for transplanting dynamical loops for protein engineering. PMID:35438789
Cryo-EM structure of glycoprotein C from Crimean-Congo hemorrhagic fever virus. PMID:35234630
The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and X-ray diffraction at room temperature. PMID:35169801
Protein sequence design with a learned potential. PMID:35136054
Quantifying structural relationships of metal-binding sites suggests origins of biological electron transfer. PMID:35030025
Helical structure motifs made searchable for functional peptide design. PMID:35013238
Biological factors in the synthetic construction of overlapping genes. PMID:34895142
Assessing the accuracy of contact and distance predictions in CASP14. PMID:34595772
Socket2: A Program for Locating, Visualising, and Analysing Coiled-coil Interfaces in Protein Structures. PMID:34498035
Poor Person's pH Simulation of Membrane Proteins. PMID:34302678
Identification and Characterization of Specific Protein-Lipid Interactions Using Molecular Simulation. PMID:34302674
Deep Learning for Protein-Protein Interaction Site Prediction. PMID:34236667
Structural basis for the constitutive activity and immunomodulatory properties of the Epstein-Barr virus-encoded G protein-coupled receptor BILF1. PMID:34216564
Micro-Aqueous Organic System: A Neglected Model in Computational Lipase Design? PMID:34200257
Functional and structural analyses of novel Smith-Kingsmore Syndrome-Associated MTOR variants reveal potential new mechanisms and predictors of pathogenicity. PMID:34197453
Engineering the protein dynamics of an ancestral luciferase. PMID:34127663
The structural heterogeneity of α-synuclein is governed by several distinct subpopulations with interconversion times slower than milliseconds. PMID:34015255
Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. PMID:33925854
Genome-editing approaches and applications: a brief review on CRISPR technology and its role in cancer. PMID:33732568
In silico method for selecting residue pairs for single-molecule microscopy and spectroscopy. PMID:33707507
Fisetin inhibits tau aggregation by interacting with the protein and preventing the formation of β-strands. PMID:33662414
SARS-CoV-2 spillover transmission due to recombination event. PMID:33615041
Are vanadium complexes druggable against the main protease Mpro of SARS-CoV-2? - A computational approach. PMID:33589845
Study on mechanism of matrine in treatment of COVID-19 combined with liver injury by network pharmacology and molecular docking technology. PMID:33517789
A structural and kinetic survey of GH5_4 endoglucanases reveals determinants of broad substrate specificity and opportunities for biomass hydrolysis. PMID:33454012
Exploring the Evolutionary History of Kinetic Stability in the α-Lytic Protease Family. PMID:33433210
Evaluating Protein Transfer Learning with TAPE. PMID:33390682
PremPS: Predicting the impact of missense mutations on protein stability. PMID:33378330
Disclosing the Interaction of Gold Nanoparticles with Aβ(1-40) Monomers through Replica Exchange Molecular Dynamics Simulations. PMID:33375086
Characterization of the Mycobacterial MSMEG-3762/63 Efflux Pump in Mycobacterium smegmatis Drug Efflux. PMID:33343518
Autochthonous Transmission of West Nile Virus by a New Vector in Iran, Vector-Host Interaction Modeling and Virulence Gene Determinants. PMID:33339336
Genetic interaction mapping informs integrative structure determination of protein complexes. PMID:33303586
MMP activation-associated aminopeptidase N reveals a bivalent 14-3-3 binding motif. PMID:33109610
Effects of Nucleotide and End-Dependent Actin Conformations on Polymerization. PMID:33080221
A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry. PMID:32857966
Structure of human Frizzled5 by fiducial-assisted cryo-EM supports a heterodimeric mechanism of canonical Wnt signaling. PMID:32762848
PremPRI: Predicting the Effects of Missense Mutations on Protein-RNA Interactions. PMID:32756481
Insights into the Effect of Curcumin and (-)-Epigallocatechin-3-Gallate on the Aggregation of Aβ(1-40) Monomers by Means of Molecular Dynamics. PMID:32751722
Side chain flexibility and the symmetry of protein homodimers. PMID:32706779
Insight into vitronectin structural evolution on material surface chemistries: The mediation for cell adhesion. PMID:32695935
High-Resolution XFEL Structure of the Soluble Methane Monooxygenase Hydroxylase Complex with its Regulatory Component at Ambient Temperature in Two Oxidation States. PMID:32683863
Structure-based designing efficient peptides based on p53 binding site residues to disrupt p53-MDM2/X interaction. PMID:32651397
On the complementarity of X-ray and NMR data. PMID:32647823
Structure and Dynamics in the ATG8 Family From Experimental to Computational Techniques. PMID:32587856
Coarse-grained (hybrid) integrative modeling of biomolecular interactions. PMID:32514329
High-Strength, Durable All-Silk Fibroin Hydrogels with Versatile Processability toward Multifunctional Applications. PMID:32440259
The Cell Wall PAC (Proline-Rich, Arabinogalactan Proteins, Conserved Cysteines) Domain-Proteins Are Conserved in the Green Lineage. PMID:32260156
Sonification based de novo protein design using artificial intelligence, structure prediction, and analysis using molecular modeling. PMID:32206742
Mutation effect estimation on protein-protein interactions using deep contextualized representation learning. PMID:32166223
Effect of Phosphorylation and O-GlcNAcylation on Proline-Rich Domains of Tau. PMID:32065850
Structural and biophysical characterization of the type VII collagen vWFA2 subdomain leads to identification of two binding sites. PMID:32031736
Human αB-crystallin discriminates between aggregation-prone and function-preserving variants of a client protein. PMID:31812542
Sequence-Derived Markers of Drug Targets and Potentially Druggable Human Proteins. PMID:31803227
Well-Balanced Force Field ff03CMAP for Folded and Disordered Proteins. PMID:31657215
Tuning Structure and Dynamics of Blue Copper Azurin Junctions via Single Amino-Acid Mutations. PMID:31618974
Molecular recognition of ubiquitin and Lys63-linked diubiquitin by STAM2 UIM-SH3 dual domain: the effect of its linker length and flexibility. PMID:31601934
SSEThread: Integrative threading of the DNA-PKcs sequence based on data from chemical cross-linking and hydrogen deuterium exchange. PMID:31570166
Biophysical Insight on the Membrane Insertion of an Arginine-Rich Cell-Penetrating Peptide. PMID:31505894
Modulation of Amyloid-β42 Conformation by Small Molecules Through Nonspecific Binding. PMID:31476124
Conformational Ensembles Exhibit Extensive Molecular Recognition Features. PMID:31459119
rawMSA: End-to-end Deep Learning using raw Multiple Sequence Alignments. PMID:31415569
Comparative structural and thermal stability studies of Cuc m 2.0101, Art v 4.0101 and other allergenic profilins. PMID:31326654
CAGI5: Objective performance assessments of predictions based on the Evolutionary Action equation. PMID:31317604
Prediction of interresidue contacts with DeepMetaPSICOV in CASP13. PMID:31298436
Comparative Exploratory Analysis of Intrinsically Disordered Protein Dynamics Using Machine Learning and Network Analytic Methods. PMID:31245383
ProteinNet: a standardized data set for machine learning of protein structure. PMID:31185886
PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact. PMID:31161204
PrankWeb: a web server for ligand binding site prediction and visualization. PMID:31114880
Regulation of measles virus gene expression by P protein coiled-coil properties. PMID:31086822
Single nucleotide polymorphisms in the human ATP7B gene modify the properties of the ATP7B protein. PMID:31070637
Essential Mycoplasma Glycolipid Synthase Adheres to the Cell Membrane by Means of an Amphipathic Helix. PMID:31068620
Deep Mutational Scan of the Highly Conserved Influenza A Virus M1 Matrix Protein Reveals Substantial Intrinsic Mutational Tolerance. PMID:31019050
Prediction of VRC01 neutralization sensitivity by HIV-1 gp160 sequence features. PMID:30933973
The disordered plant dehydrin Lti30 protects the membrane during water-related stress by cross-linking lipids. PMID:30819802
Structural Analysis of a Trimer of β2-Microgloblin Fragment by Molecular Dynamics Simulations. PMID:30771855
Homogentisate 1,2-dioxygenase (HGD) gene variants, their analysis and genotype-phenotype correlations in the largest cohort of patients with AKU. PMID:30737480
Proline 411 biases the conformation of the intrinsically disordered plant UVR8 photoreceptor C27 domain altering the functional properties of the peptide. PMID:30692548
ATP-induced asymmetric pre-protein folding as a driver of protein translocation through the Sec machinery. PMID:30601115
Helical Structure of Recombinant Melittin. PMID:30570258
RIP-MD: a tool to study residue interaction networks in protein molecular dynamics. PMID:30568854
Fine mapping of hydrophobic contacts reassesses the organization of the first three dystrophin coiled-coil repeats. PMID:30468271
Prediction of Antimicrobial Potential of a Chemically Modified Peptide From Its Tertiary Structure. PMID:30416494
Automatically Fixing Errors in Glycoprotein Structures with Rosetta. PMID:30344107
Machine Learning Approaches for Protein⁻Protein Interaction Hot Spot Prediction: Progress and Comparative Assessment. PMID:30287797
Two distinct conformations of factor H regulate discrete complement-binding functions in the fluid phase and at cell surfaces. PMID:30217822
DaReUS-Loop: accurate loop modeling using fragments from remote or unrelated proteins. PMID:30209260
Enhanced ER proteostasis and temperature differentially impact the mutational tolerance of influenza hemagglutinin. PMID:30188321
Structural Characterization of the Lactobacillus Plantarum FlmC Protein Involved in Biofilm Formation. PMID:30181476
Predicting the clinical impact of human mutation with deep neural networks. PMID:30038395
A coarse-grained approach to studying the interactions of the antimicrobial peptides aurein 1.2 and maculatin 1.1 with POPG/POPE lipid mixtures. PMID:30019106
Hsp90 shapes protein and RNA evolution to balance trade-offs between protein stability and aggregation. PMID:29725062
The Preservation of Lyophilized Human Growth Hormone Activity: how Do Buffers and Sugars Interact? PMID:29700627
Supramolecular self assembly of nanodrill-like structures for intracellular delivery. PMID:29501722
Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein-Protein Binding Affinity upon Mutation. PMID:29401388
Structure-function insights into direct lipid transfer between membranes by Mmm1-Mdm12 of ERMES. PMID:29279306
The Cryoelectron Microscopy Structure of the Type 1 Chaperone-Usher Pilus Rod. PMID:29129382
Differential Interaction of Antimicrobial Peptides with Lipid Structures Studied by Coarse-Grained Molecular Dynamics Simulations. PMID:29053635
Systematic Identification of Machine-Learning Models Aimed to Classify Critical Residues for Protein Function from Protein Structure. PMID:28991206
Enhancing Structure Prediction and Design of Soluble and Membrane Proteins with Explicit Solvent-Protein Interactions. PMID:28966016
Host proteostasis modulates influenza evolution. PMID:28949290
Investigating Ebola virus pathogenicity using molecular dynamics. PMID:28812539
Catabolism of the Cholesterol Side Chain in Mycobacterium tuberculosis Is Controlled by a Redox-Sensitive Thiol Switch. PMID:28786661
Structural insights into the function of ZRANB3 in replication stress response. PMID:28621305
Distribution of dipeptides in different protein structural classes: an effort to find new similarities. PMID:28612124
Albumin (BSA) adsorption onto graphite stepped surfaces. PMID:28595417
How do SMA-linked mutations of SMN1 lead to structural/functional deficiency of the SMA protein? PMID:28570645
Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction. PMID:28453681
The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins. PMID:28448138
Crystal structure of a small heat-shock protein from Xylella fastidiosa reveals a distinct high-order structure. PMID:28368281
Alteration of the α1β2/α2β1 subunit interface contributes to the increased hemoglobin-oxygen affinity of high-altitude deer mice. PMID:28362841
An integrated Java tool for generating amino acid sequence alignments with mapped secondary structure elements. PMID:28324365
Twilight reloaded: the peptide experience. PMID:28291756
Computational smart polymer design based on elastin protein mutability. PMID:28279921
Interaction of aurein 1.2 and its analogue with DPPC lipid bilayer. PMID:28130642
One-Way Allosteric Communication between the Two Disulfide Bonds in Tissue Factor. PMID:28076818
Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis. PMID:27803181
Death Receptor 5 Networks Require Membrane Cholesterol for Proper Structure and Function. PMID:27720987
GlycoMinestruct: a new bioinformatics tool for highly accurate mapping of the human N-linked and O-linked glycoproteomes by incorporating structural features. PMID:27708373
Structural and Functional Basis for Lipid Synergy on the Activity of the Antibacterial Peptide ABC Transporter McjD. PMID:27555327
The Ramachandran Number: An Order Parameter for Protein Geometry. PMID:27490241
ff14IDPs force field improving the conformation sampling of intrinsically disordered proteins. PMID:27484738
Computational studies of human class V alcohol dehydrogenase - the odd sibling. PMID:27455956
Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds. PMID:27437113
Molecular Dynamics Driven Design of pH-Stabilized Mutants of MNEI, a Sweet Protein. PMID:27340829
Sequence- and Structure-Based Analysis of Tissue-Specific Phosphorylation Sites. PMID:27332813
MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions. PMID:27150810
Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes. PMID:27138088
Automated structure modeling of large protein assemblies using crosslinks as distance restraints. PMID:27111507
Engineered human angiogenin mutations in the placental ribonuclease inhibitor complex for anticancer therapy: Insights from enhanced sampling simulations. PMID:27110669
Viral Evolved Inhibition Mechanism of the RNA Dependent Protein Kinase PKR's Kinase Domain, a Structural Perspective. PMID:27088597
Structure-Guided Mutations in the Terminal Organelle Protein MG491 Cause Major Motility and Morphologic Alterations on Mycoplasma genitalium. PMID:27082435
Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications. PMID:27028541
Conserved differences in protein sequence determine the human pathogenicity of Ebolaviruses. PMID:27009368
Application of Rigidity Theory to the Thermostabilization of Lipase A from Bacillus subtilis. PMID:27003415
Unlocking the Bacterial SecY Translocon. PMID:26973090
Characterization of parasite-specific indels and their proposed relevance for selective anthelminthic drug targeting. PMID:26829384
All-atom molecular dynamics analysis of multi-peptide systems reproduces peptide solubility in line with experimental observations. PMID:26817663
The effect of amidation on the behaviour of antimicrobial peptides. PMID:26745958
Long range Trp-Trp interaction initiates the folding pathway of a pro-angiogenic β-hairpin peptide. PMID:26602442
Insight into Early-Stage Unfolding of GPI-Anchored Human Prion Protein. PMID:26588568
BioDB extractor: customized data extraction system for commonly used bioinformatics databases. PMID:26516349
An Exploration of the Universe of Polyglutamine Structures. PMID:26495838
Functional Advantages of Conserved Intrinsic Disorder in RNA-Binding Proteins. PMID:26439842
Structure and function of the Escherichia coli Tol-Pal stator protein TolR. PMID:26354441
Cardiolipin Interactions with Proteins. PMID:26300339
Membrane Interaction of the Glycosyltransferase WaaG. PMID:26244737
Secondary Structure of Rat and Human Amylin across Force Fields. PMID:26221949
Identification of a Class of Protein ADP-Ribosylating Sirtuins in Microbial Pathogens. PMID:26166706
Multi-level machine learning prediction of protein-protein interactions in Saccharomyces cerevisiae. PMID:26157620
Structural Rigidity and Protein Thermostability in Variants of Lipase A from Bacillus subtilis. PMID:26147762
Elucidation of Ligand-Dependent Modulation of Disorder-Order Transitions in the Oncoprotein MDM2. PMID:26046940
CleavPredict: A Platform for Reasoning about Matrix Metalloproteinases Proteolytic Events. PMID:25996941
Test and Evaluation of ff99IDPs Force Field for Intrinsically Disordered Proteins. PMID:25919886
Predicting a double mutant in the twilight zone of low homology modeling for the skeletal muscle voltage-gated sodium channel subunit beta-1 (Nav1.4 β1). PMID:25904995
Key challenges for the creation and maintenance of specialist protein resources. PMID:25820941
Statistical dictionaries for hypothetical in silico model of the early-stage intermediate in protein folding. PMID:25808133
Patterns of structural and sequence variation within isotype lineages of the Neisseria meningitidis transferrin receptor system. PMID:25800619
Phosphorylation of Atg31 is required for autophagy. PMID:25773276
A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction. PMID:25750595
The effect of ligands on the thermal stability of sulfotransferases: a molecular dynamics simulation study. PMID:25750022
Structures of the Apo and FAD-bound forms of 2-hydroxybiphenyl 3-monooxygenase (HbpA) locate activity hotspots identified by using directed evolution. PMID:25737306
Structural and functional investigation of flavin binding center of the NqrC subunit of sodium-translocating NADH:quinone oxidoreductase from Vibrio harveyi. PMID:25734798
Protein models docking benchmark 2. PMID:25712716
Structural transitions and interactions in the early stages of human glucagon amyloid fibrillation. PMID:25692598
Comparison of three ionic liquid-tolerant cellulases by molecular dynamics. PMID:25692593
Structural and biochemical analysis of the essential diadenylate cyclase CdaA from Listeria monocytogenes. PMID:25605729
An approach to creating a more realistic working model from a protein data bank entry. PMID:25605595
Flies expand the repertoire of protein structures that bind ice. PMID:25561557
Fragment based group QSAR and molecular dynamics mechanistic studies on arylthioindole derivatives targeting the α-β interfacial site of human tubulin. PMID:25521775
The structural basis for receptor recognition of human interleukin-18. PMID:25500532
FadA5 a thiolase from Mycobacterium tuberculosis: a steroid-binding pocket reveals the potential for drug development against tuberculosis. PMID:25482540
ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank. PMID:25392418
Analysis of nidogen-1/laminin γ1 interaction by cross-linking, mass spectrometry, and computational modeling reveals multiple binding modes. PMID:25387007
Exploring nicotinamide cofactor promiscuity in NAD(P)H-dependent flavin containing monooxygenases (FMOs) using natural variation within the phosphate binding loop. Structure and activity of FMOs from Cellvibrio sp. BR and Pseudomonas stutzeri NF13. PMID:25383040
Characteristics of protein residue-residue contacts and their application in contact prediction. PMID:25374390
Structural states of the flexible catalytic loop of M. tuberculosis tyrosyl-tRNA synthetase in different enzyme-substrate complexes. PMID:25373444
A series of PDB-related databanks for everyday needs. PMID:25352545
Structures of Arg- and Gln-type bacterial cysteine dioxygenase homologs. PMID:25307852
Investigation of the Josephin Domain protein-protein interaction by molecular dynamics. PMID:25268243
Random forest-based protein model quality assessment (RFMQA) using structural features and potential energy terms. PMID:25222008
Structure and regulatory interactions of the cytoplasmic terminal domains of serotonin transporter. PMID:25093911
An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs. PMID:25063439
In silico comparative characterization of pharmacogenomic missense variants. PMID:25057096
The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin. PMID:25006036
PCASSO: a fast and efficient Cα-based method for accurately assigning protein secondary structure elements. PMID:24995959
Structural heterogeneity in transmembrane amyloid precursor protein homodimer is a consequence of environmental selection. PMID:24926593
ParaPep: a web resource for experimentally validated antiparasitic peptide sequences and their structures. PMID:24923818
Factors that drive peptide assembly from native to amyloid structures: experimental and theoretical analysis of [leu-5]-enkephalin mutants. PMID:24915112
VarMod: modelling the functional effects of non-synonymous variants. PMID:24906884
Probing the average local structure of biomolecules using small-angle scattering and scaling laws. PMID:24896127
Prediction and redesign of protein-protein interactions. PMID:24878423
An experimentally determined evolutionary model dramatically improves phylogenetic fit. PMID:24859245
Structural insights into the evolution of a sexy protein: novel topology and restricted backbone flexibility in a hypervariable pheromone from the red-legged salamander, Plethodon shermani. PMID:24849290
Structure of a sedoheptulose 7-phosphate cyclase: ValA from Streptomyces hygroscopicus. PMID:24832673
Alpha-bulges in G protein-coupled receptors. PMID:24806342
PredictProtein--an open resource for online prediction of protein structural and functional features. PMID:24799431
Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase. PMID:24742328
The DynaMine webserver: predicting protein dynamics from sequence. PMID:24728994
Anomalies in the refinement of isoleucine. PMID:24699648
Molecular mechanism of Mg2+-dependent gating in CorA. PMID:24694723
A rapid, site-selective and efficient route to the dual modification of DARPins. PMID:24687090
A molecular interpretation of 2D IR protein folding experiments with Markov state models. PMID:24655511
Insight into conformational change for 14-3-3σ protein by molecular dynamics simulation. PMID:24552877
Folding of the RNA recognition motif (RRM) domains of the amyotrophic lateral sclerosis (ALS)-linked protein TDP-43 reveals an intermediate state. PMID:24497641
Protein NMR structures refined with Rosetta have higher accuracy relative to corresponding X-ray crystal structures. PMID:24392845
Protein domains of unknown function are essential in bacteria. PMID:24381303
GPCRDB: an information system for G protein-coupled receptors. PMID:24304901
Hemolytik: a database of experimentally determined hemolytic and non-hemolytic peptides. PMID:24174543
Optimized atomic statistical potentials: assessment of protein interfaces and loops. PMID:24078704
Quality assessment of protein NMR structures. PMID:24060334
A conserved motif flags acyl carrier proteins for β-branching in polyketide synthesis. PMID:24056399
Molecular dynamics simulations on the Tre1 G protein-coupled receptor: exploring the role of the arginine of the NRY motif in Tre1 structure. PMID:24044607
Exploiting tertiary structure through local folds for crystallographic phasing. PMID:24037245
Conformational stability of fibrillar amyloid-beta oligomers via protofilament pair formation - a systematic computational study. PMID:23936224
An overview of tools for the validation of protein NMR structures. PMID:23877928
Structural analysis of mitochondrial mutations reveals a role for bigenomic protein interactions in human disease. PMID:23874847
Conformational stability and activity analysis of two hydroxymethylbilane synthase mutants, K132N and V215E, with different phenotypic association with acute intermittent porphyria. PMID:23815679
Aβ monomers transiently sample oligomer and fibril-like configurations: ensemble characterization using a combined MD/NMR approach. PMID:23811057
Structural and functional characterization of Pseudomonas aeruginosa AlgX: role of AlgX in alginate acetylation. PMID:23779107
nfxB as a novel target for analysis of mutation spectra in Pseudomonas aeruginosa. PMID:23762483
VLDP web server: a powerful geometric tool for analysing protein structures in their environment. PMID:23761450
Structure-based comparative analysis and prediction of N-linked glycosylation sites in evolutionarily distant eukaryotes. PMID:23459159
New enumeration algorithm for protein structure comparison and classification. PMID:23445440
Designing and benchmarking the MULTICOM protein structure prediction system. PMID:23442819
Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles? PMID:23442792
The activity of prolactin releasing peptide correlates with its helicity. PMID:23426574
Mining tertiary structural motifs for assessment of designability. PMID:23422424
Discovery of novel Trypanosoma brucei phosphodiesterase B1 inhibitors by virtual screening against the unliganded TbrPDEB1 crystal structure. PMID:23409953
Predicting functional effect of human missense mutations using PolyPhen-2. PMID:23315928
Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding. PMID:23262490
Modelling dynamics in protein crystal structures by ensemble refinement. PMID:23251785
Structure and dynamics of the second CARD of human RIG-I provide mechanistic insights into regulation of RIG-I activation. PMID:23063562
In silico modeling of the staphylococcal bacteriophage-derived peptidase CHAP(K). PMID:23050213
Structural differences between thermophilic and mesophilic membrane proteins. PMID:23001966
CING: an integrated residue-based structure validation program suite. PMID:22986687
Are long-range structural correlations behind the aggregration phenomena of polyglutamine diseases? PMID:22577357
Systematic analysis of metallo-β-lactamases using an automated database. PMID:22547615
Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen. PMID:22505400
Another case of fraud in structural biology. PMID:22505399
PDB_REDO: constructive validation, more than just looking for errors. PMID:22505269
MSV3d: database of human MisSense Variants mapped to 3D protein structure. PMID:22491796
Comparative molecular dynamics simulations of the antimicrobial peptide CM15 in model lipid bilayers. PMID:22387432
ccPDB: compilation and creation of data sets from Protein Data Bank. PMID:22139939
Multi-scale genetic dynamic modelling I : an algorithm to compute generators. PMID:21487823
The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. PMID:21177655
A series of PDB-related databanks for everyday needs PubMed citations: 211.

211 articles citing: A series of PDB-related databanks for everyday needs

Contiguously hydrophobic sequences are functionally significant throughout the human exome. PMID:35294280
Structural modeling of human AKAP3 protein and in silico analysis of single nucleotide polymorphisms associated with sperm motility. PMID:35256641
Ruffling is essential for Staphylococcus aureus IsdG-catalyzed degradation of heme to staphylobilin. PMID:35247855
A new inactive conformation of SARS-CoV-2 main protease. PMID:35234150
Design of a mutation-integrated trimeric RBD with broad protection against SARS-CoV-2. PMID:35169113
Proteome-scale mapping of binding sites in the unstructured regions of the human proteome. PMID:35044719
PEA-15 engages in allosteric interactions using a common scaffold in a phosphorylation-dependent manner. PMID:34997083
The Stimulatory Effects of Intracellular α-Synuclein on Synaptic Transmission Are Attenuated by 2-Octahydroisoquinolin-2(1H)-ylethanamine. PMID:34948050
Missense Mutations Modify the Conformational Ensemble of the α-Synuclein Monomer Which Exhibits a Two-Phase Characteristic. PMID:34912851
DE-STRESS: a user-friendly web application for the evaluation of protein designs. PMID:34908138
Evolutionary Dynamics of Indels in SARS-CoV-2 Spike Glycoprotein. PMID:34898980
Repeated MDA5 Gene Loss in Birds: An Evolutionary Perspective. PMID:34834938
Discovering the Ultimate Limits of Protein Secondary Structure Prediction. PMID:34827624
Destabilization of the Alzheimer's amyloid-β peptide by a proline-rich β-sheet breaker peptide: a molecular dynamics simulation study. PMID:34796404
Natural Products-Based Drug Design against SARS-CoV-2 Mpro 3CLpro. PMID:34769170
A Deep Learning and XGBoost-Based Method for Predicting Protein-Protein Interaction Sites. PMID:34764983
Visualized and Quantitative Conformational Analysis of Peptidomimetics. PMID:34661014
Comprehensive analysis of lectin-glycan interactions reveals determinants of lectin specificity. PMID:34613971
Identification of Oleanolic Acid as Allosteric Agonist of Integrin αM by Combination of In Silico Modeling and In Vitro Analysis. PMID:34603018
Insights into Comparative Modeling of VHH Domains. PMID:34575931
How do I get the most out of my protein sequence using bioinformatics tools? PMID:34473083
Simulating PIP2-Induced Gating Transitions in Kir6.2 Channels. PMID:34447786
Tissue-Nonspecific Alkaline Phosphatase (TNAP) as the Enzyme Involved in the Degradation of Nucleotide Analogues in the Ligand Docking and Molecular Dynamics Approaches. PMID:34439771
Structural and Genomic Insights Into Pyrazinamide Resistance in Mycobacterium tuberculosis Underlie Differences Between Ancient and Modern Lineages. PMID:34422898
DisCoTune: versatile auxiliary plasmids for the production of disulphide-containing proteins and peptides in the E. coli T7 system. PMID:34405535
Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. PMID:34337269
The N-terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition. PMID:34137249
Critical assessment of coiled-coil predictions based on protein structure data. PMID:34127723
In Silico Evaluation of Cyclophilin Inhibitors as Potential Treatment for SARS-CoV-2. PMID:34109257
Assessing the Role of Calmodulin's Linker Flexibility in Target Binding. PMID:34066691
Bridging between material properties of proteins and the underlying molecular interactions. PMID:33951045
Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator. PMID:33904398
Multi-Scale Flexible Fitting of Proteins to Cryo-EM Density Maps at Medium Resolution. PMID:33842541
MENSAdb: a thorough structural analysis of membrane protein dimers. PMID:33822911
Huntingtin: A Protein with a Peculiar Solvent Accessible Surface. PMID:33809039
Age-dependent ataxia and neurodegeneration caused by an αII spectrin mutation with impaired regulation of its calpain sensitivity. PMID:33790315
Understanding the Origins of Loss of Protein Function by Analyzing the Effects of Thousands of Variants on Activity and Abundance. PMID:33779753
Mechanistic insights into the adsorption and bioactivity of fibronectin on surfaces with varying chemistries by a combination of experimental strategies and molecular simulations. PMID:33778193
In-silico screening for identification of potential inhibitors against SARS-CoV-2 transmembrane serine protease 2 (TMPRSS2). PMID:33775827
Considerations Regarding Activity Determinants of Fungal Polyphenol Oxidases Based on Mutational and Structural Studies. PMID:33741634
Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network. PMID:33718433
The p.Ala2430Val mutation in filamin C causes a "hypertrophic myofibrillar cardiomyopathy". PMID:33710525
A comparative study of protein-ssDNA interactions. PMID:33655206
Statistical Evidence for a Helical Nascent Chain. PMID:33652806
GraphBind: protein structural context embedded rules learned by hierarchical graph neural networks for recognizing nucleic-acid-binding residues. PMID:33577689
Computed optical spectra of SARS-CoV-2 proteins. PMID:33518776
Bridging Themes: Short Protein Segments Found in Different Architectures. PMID:33502503
Cancer associated talin point mutations disorganise cell adhesion and migration. PMID:33431906
LAHMA: structure analysis through local annotation of homology-matched amino acids. PMID:33404523
Massively parallel functional testing of MSH2 missense variants conferring Lynch syndrome risk. PMID:33357406
Molecular Mechanisms of Activation in the Orange Carotenoid Protein Revealed by Molecular Dynamics. PMID:33332967
PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins. PMID:33305318
SSSCPreds: Deep Neural Network-Based Software for the Prediction of Conformational Variability and Application to SARS-CoV-2. PMID:33283104
A pleurocidin analogue with greater conformational flexibility, enhanced antimicrobial potency and in vivo therapeutic efficacy. PMID:33247193
EspcTM: Kinetic Transition Network Based on Trajectory Mapping in Effective Energy Rescaling Space. PMID:33195438
A Proline-Based Tectons and Supramolecular Synthons for Drug Design 2.0: A Case Study of ACEI. PMID:33114370
Real-time tracking of protein unfolding with time-resolved x-ray solution scattering. PMID:32984436
Structural insights into the histidine-containing phospho-transfer protein and receiver domain of sensor histidine kinase suggest a complex model in the two-component regulatory system in Pseudomonas aeruginosa. PMID:32939285
Transient Unfolding and Long-Range Interactions in Viral BCL2 M11 Enable Binding to the BECN1 BH3 Domain. PMID:32932757
Structural basis for the core-mannan biosynthesis of cell wall fungal-type galactomannan in Aspergillus fumigatus. PMID:32873705
Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact. PMID:32870157
Influence of the amino-terminal sequence on the structure and function of HIV integrase. PMID:32867805
Evidence that the TRPV1 S1-S4 membrane domain contributes to thermosensing. PMID:32820172
Crystal structure of GCN5 PCAF N-terminal domain reveals atypical ubiquitin ligase structure. PMID:32820047
Tyrosine Nitration Contributes to Nitric Oxide-Stimulated Degradation of CYP2B6. PMID:32817462
Global alignment and assessment of TRP channel transmembrane domain structures to explore functional mechanisms. PMID:32804077
Association between flower stalk elongation, an Arabidopsis developmental trait, and the subcellular location and movement dynamics of the nonstructural protein P3 of Turnip mosaic virus. PMID:32737952
Side chain flexibility and the symmetry of protein homodimers. PMID:32706779
Structure of the Regulatory Cytosolic Domain of a Eukaryotic Potassium-Chloride Cotransporter. PMID:32679039
Structural Characterization of Black Widow Spider Dragline Silk Proteins CRP1 and CRP4. PMID:32674428
Dynamical Behavior and Conformational Selection Mechanism of the Intrinsically Disordered Sic1 Kinase-Inhibitor Domain. PMID:32664566
iPNHOT: a knowledge-based approach for identifying protein-nucleic acid interaction hot spots. PMID:32631222
Glutantβase: a database for improving the rational design of glucose-tolerant β-glucosidases. PMID:32611314
The complex role of the N-terminus and acidic residues of HdeA as pH-dependent switches in its chaperone function. PMID:32593908
Non-cooperative 4E-BP2 folding with exchange between eIF4E-binding and binding-incompatible states tunes cap-dependent translation inhibition. PMID:32561718
AllesTM: predicting multiple structural features of transmembrane proteins. PMID:32532211
Coarse-grained (hybrid) integrative modeling of biomolecular interactions. PMID:32514329
Aggregation of M3 (E376D) variant of alpha1- antitrypsin. PMID:32427833
A terminal α3-galactose modification regulates an E3 ubiquitin ligase subunit in Toxoplasma gondii. PMID:32414843
Caretta - A multiple protein structure alignment and feature extraction suite. PMID:32368333
FTIR Spectroscopy Study of the Secondary Structure Changes in Human Serum Albumin and Trypsin under Neutral Salts. PMID:32295172
Outlier Profiles of Atomic Structures Derived from X-ray Crystallography and from Cryo-Electron Microscopy. PMID:32231015
Data set of intrinsically disordered proteins analysed at a local protein conformation level. PMID:32195305
Structural Basis of Ca2+-Dependent Self-Processing Activity of Repeat-in-Toxin Proteins. PMID:32184239
Unconventional Secondary Structure Mimics: Ladder-Rungs. PMID:32176815
Structural basis for recognition of RALF peptides by LRX proteins during pollen tube growth. PMID:32165538
ALEPH: a network-oriented approach for the generation of fragment-based libraries and for structure interpretation. PMID:32133985
PlantPepDB: A manually curated plant peptide database. PMID:32042035
Mitochondrial localization of Dictyostelium discoideum dUTPase mediated by its N-terminus. PMID:31910901
Structural analysis of mycobacterial homoserine transacetylases central to methionine biosynthesis reveals druggable active site. PMID:31889085
Amyloid beta oligomers: how pH influences over trimer and pentamer structures? PMID:31834477
Design of a Helical-Stabilized, Cyclic, and Nontoxic Analogue of the Peptide Cm-p5 with Improved Antifungal Activity. PMID:31763531
Using Structural Analysis In Silico to Assess the Impact of Missense Variants in MEN1. PMID:31737856
Protein Stability in Titan's Subsurface Water Ocean. PMID:31730377
Spectroscopic Evidence for Electronic Control of Heme Hydroxylation by IsdG. PMID:31693363
Sequence and Structure Properties Uncover the Natural Classification of Protein Complexes Formed by Intrinsically Disordered Proteins via Mutual Synergistic Folding. PMID:31683980
New insights into protein-DNA binding specificity from hydrogen bond based comparative study. PMID:31665426
The Sequence and a Three-Dimensional Structural Analysis Reveal Substrate Specificity Among Snake Venom Phosphodiesterases. PMID:31661911
ProtMiscuity: a database of promiscuous proteins. PMID:31650170
Structural characterization of HypX responsible for CO biosynthesis in the maturation of NiFe-hydrogenase. PMID:31646188
Less Is More: Coarse-Grained Integrative Modeling of Large Biomolecular Assemblies with HADDOCK. PMID:31539250
Deep Mutational Scanning Comprehensively Maps How Zika Envelope Protein Mutations Affect Viral Growth and Antibody Escape. PMID:31511387
Comparative Study on Hyaluronic Acid Binding to Murine SAA1.1 and SAA2.2. PMID:31460467
C-Terminal Plays as the Possible Nucleation of the Self-Aggregation of the S-Shape Aβ11-42 Tetramer in Solution: Intensive MD Study. PMID:31460204
Systematic FTIR Spectroscopy Study of the Secondary Structure Changes in Human Serum Albumin under Various Denaturation Conditions. PMID:31409012
In Vitro Double-Stranded RNA Synthesis by Rotavirus Polymerase Mutants with Lesions at Core Shell Contact Sites. PMID:31341048
The structural characterization of a glucosylglycerate hydrolase provides insights into the molecular mechanism of mycobacterial recovery from nitrogen starvation. PMID:31316802
Atomistic Insights into the Functional Instability of the Second Helix of Fatty Acid Binding Protein. PMID:31301805
Characterization of two putative Dichelobacter nodosus footrot vaccine antigens identifies the first lysozyme inhibitor in the genus. PMID:31296905
DDGun: an untrained method for the prediction of protein stability changes upon single and multiple point variations. PMID:31266447
Burkholderia pseudomallei d-alanine-d-alanine ligase; detailed characterisation and assessment of a potential antibiotic drug target. PMID:31260169
2StrucCompare: a webserver for visualizing small but noteworthy differences between protein tertiary structures through interrogation of the secondary structure content. PMID:31114904
Structural basis for catalysis and substrate specificity of a 3C-like cysteine protease from a mosquito mesonivirus. PMID:31078932
Building and rebuilding N-glycans in protein structure models. PMID:30988258
Structure of ATP citrate lyase and the origin of citrate synthase in the Krebs cycle. PMID:30944476
Correlations between secondary structure- and protein-protein interface-mimicry: the interface mimicry hypothesis. PMID:30847453
A new clustering and nomenclature for beta turns derived from high-resolution protein structures. PMID:30845191
Benchmarking of different molecular docking methods for protein-peptide docking. PMID:30717654
Computational design of symmetrical eight-bladed β-propeller proteins. PMID:30713702
ccPDB 2.0: an updated version of datasets created and compiled from Protein Data Bank. PMID:30689843
Structure-Guided Exploration of SDS22 Interactions with Protein Phosphatase PP1 and the Splicing Factor BCLAF1. PMID:30661852
Structure, Mechanism, and Inhibition of Aspergillus fumigatus Thioredoxin Reductase. PMID:30642940
Structure of the SLy1 SAM homodimer reveals a new interface for SAM domain self-association. PMID:30631134
Low Postseroconversion CD4+ T-cell Level Is Associated with Faster Disease Progression and Higher Viral Evolutionary Rate in HIV-2 Infection. PMID:30622192
Characteristics of interactions at protein segments without non-local intramolecular contacts in the Protein Data Bank. PMID:30537764
Molecular dynamics simulation of the follicle-stimulating hormone receptor. Understanding the conformational dynamics of receptor variants at positions N680 and D408 from in silico analysis. PMID:30462715
Co-Evolution of Intrinsically Disordered Proteins with Folded Partners Witnessed by Evolutionary Couplings. PMID:30366362
Prediction of disulfide dihedral angles using chemical shifts. PMID:30310586
Circular Permutation Obscures Universality of a Ribosomal Protein. PMID:30306205
Crystal structure and functional analysis of human C1ORF123. PMID:30280012
Etersalate prevents the formations of 6Aβ16-22 oligomer: An in silico study. PMID:30226897
The lipid environment determines the activity of the Escherichia coli ammonium transporter AmtB. PMID:30211659
Differences in antigenic sites and other functional regions between genotype A and G mumps virus surface proteins. PMID:30190529
Temperature-induced collapse of a disordered peptide observed by three sampling methods in molecular dynamics simulations. PMID:30134733
Crystal Structures of R-Type Bacteriocin Sheath and Tube Proteins CD1363 and CD1364 From Clostridium difficile in the Pre-assembled State. PMID:30127773
EPO does not promote interaction between the erythropoietin and beta-common receptors. PMID:30127368
Protein-RNA interactions: structural characteristics and hotspot amino acids. PMID:30093489
A model for hydrophobic protrusions on peripheral membrane proteins. PMID:30048443
Crystal structures of two tandem malectin-like receptor kinases involved in plant reproduction. PMID:29968676
Cryo-EM structures of complex I from mouse heart mitochondria in two biochemically defined states. PMID:29915388
Cooperative Domain Formation by Homologous Motifs in HOIL-1L and SHARPIN Plays A Crucial Role in LUBAC Stabilization. PMID:29694895
A Carbohydrate Moiety of Secreted Stage-Specific Glycoprotein 4 Participates in Host Cell Invasion by Trypanosoma cruzi Extracellular Amastigotes. PMID:29692765
dbAMEPNI: a database of alanine mutagenic effects for protein-nucleic acid interactions. PMID:29688380
Structural dynamics is a determinant of the functional significance of missense variants. PMID:29610305
Active site remodeling during the catalytic cycle in metal-dependent fructose-1,6-bisphosphate aldolases. PMID:29593097
Exploring the differences and similarities between urea and thermally driven denaturation of bovine serum albumin: intermolecular forces and solvation preferences. PMID:29497866
Lipids Alter Rhodopsin Function via Ligand-like and Solvent-like Interactions. PMID:29401433
Co(II) Coordination in Prokaryotic Zinc Finger Domains as Revealed by UV-Vis Spectroscopy. PMID:29386985
Large scale analysis of protein conformational transitions from aqueous to non-aqueous media. PMID:29382320
Systematic Analysis of the Binding Surfaces between tRNAs and Their Respective Aminoacyl tRNA Synthetase Based on Structural and Evolutionary Data. PMID:29358943
Visualization and analysis of non-covalent contacts using the Protein Contacts Atlas. PMID:29335563
Characterization of Translationally Controlled Tumour Protein from the Sea Anemone Anemonia viridis and Transcriptome Wide Identification of Cnidarian Homologues. PMID:29324689
Co-precipitation molecules hemopexin and transferrin may be key molecules for fibrillogenesis in TTR V30M amyloidogenesis. PMID:29288430
Calmodulin fishing with a structurally disordered bait triggers CyaA catalysis. PMID:29287065
The dynamic dimer structure of the chaperone Trigger Factor. PMID:29222465
Quantification of the catalytic performance of C1-cellulose-specific lytic polysaccharide monooxygenases. PMID:29196788
A new parameter-rich structure-aware mechanistic model for amino acid substitution during evolution. PMID:29178386
Selective Glucocorticoid Receptor Properties of GSK866 Analogs with Cysteine Reactive Warheads. PMID:29163463
Characterizing the conformational landscape of MDM2-binding p53 peptides using Molecular Dynamics simulations. PMID:29142290
Sequence-based prediction of permissive stretches for internal protein tagging and knockdown. PMID:29084520
New insights into flavivirus biology: the influence of pH over interactions between prM and E proteins. PMID:29064083
Forecasting residue-residue contact prediction accuracy. PMID:29036497
Molecular motion regulates the activity of the Mitochondrial Serine Protease HtrA2. PMID:29022916
A distance geometry-based description and validation of protein main-chain conformation. PMID:28989721
Net Evolutionary Loss of Residue Polarity in Drosophilid Protein Cores Indicates Ongoing Optimization of Amino Acid Composition. PMID:28985302
Spatial distribution of disease-associated variants in three-dimensional structures of protein complexes. PMID:28945216
The bacterial meta-cleavage hydrolase LigY belongs to the amidohydrolase superfamily, not to the α/β-hydrolase superfamily. PMID:28935670
Conformational changes, from β-strand to α-helix, of the fatty acid-binding protein ReP1-NCXSQ in anionic lipid membranes: dependence with the vesicle curvature. PMID:28752207
Engineering protein stability with atomic precision in a monomeric miniprotein. PMID:28530710
Crystal structure and redox properties of a novel cyanobacterial heme protein with a His/Cys heme axial ligation and a Per-Arnt-Sim (PAS)-like domain. PMID:28428249
SLiMSearch: a framework for proteome-wide discovery and annotation of functional modules in intrinsically disordered regions. PMID:28387819
Substrate specificity of TOR complex 2 is determined by a ubiquitin-fold domain of the Sin1 subunit. PMID:28264193
Comparative visualization of protein secondary structures. PMID:28251875
An Extra Amino Acid Residue in Transmembrane Domain 10 of the γ-Aminobutyric Acid (GABA) Transporter GAT-1 Is Required for Efficient Ion-coupled Transport. PMID:28213519
Predicting Protein Dynamics and Allostery Using Multi-Protein Atomic Distance Constraints. PMID:28190781
Methionine residues around phosphorylation sites are preferentially oxidized in vivo under stress conditions. PMID:28079140
Domain Organization and Evolution of the Highly Divergent 5' Coding Region of Genomes of Arteriviruses, Including the Novel Possum Nidovirus. PMID:28053107
UQlust: combining profile hashing with linear-time ranking for efficient clustering and analysis of big macromolecular data. PMID:28031034
Experimental Estimation of the Effects of All Amino-Acid Mutations to HIV's Envelope Protein on Viral Replication in Cell Culture. PMID:27959955
Alpha Helices Are More Robust to Mutations than Beta Strands. PMID:27935949
A mechanism for acetylcholine receptor gating based on structure, coupling, phi, and flip. PMID:27932572
Antimicrobial Peptide Potency is Facilitated by Greater Conformational Flexibility when Binding to Gram-negative Bacterial Inner Membranes. PMID:27874065
De-novo protein function prediction using DNA binding and RNA binding proteins as a test case. PMID:27869118
A public database of macromolecular diffraction experiments. PMID:27841751
Resurrecting ancestral structural dynamics of an antiviral immune receptor: adaptive binding pocket reorganization repeatedly shifts RNA preference. PMID:27825296
Open and compressed conformations of Francisella tularensis ClpP. PMID:27802578
3DFlu: database of sequence and structural variability of the influenza hemagglutinin at population scale. PMID:27694207
Molecular modeling of Gly80 and Ser80 variants of human group IID phospholipase A2 and their receptor complexes: potential basis for weight loss in chronic obstructive pulmonary disease. PMID:27585677
G23D: Online tool for mapping and visualization of genomic variants on 3D protein structures. PMID:27565432
Order, Disorder, and Everything in Between. PMID:27548131
Carboxylic ester hydrolases: Classification and database derived from their primary, secondary, and tertiary structures. PMID:27530203
Distinct Roles of Histone H3 and H2A Tails in Nucleosome Stability. PMID:27527579
Structural Determinants of Sleeping Beauty Transposase Activity. PMID:27401040
Crystal structure and MD simulation of mouse EndoV reveal wedge motif plasticity in this inosine-specific endonuclease. PMID:27108838
Computational study of pH-dependent oligomerization and ligand binding in Alt a 1, a highly allergenic protein with a unique fold. PMID:27090909
ProViz-a web-based visualization tool to investigate the functional and evolutionary features of protein sequences. PMID:27085803
Crystal Structure and Catalytic Mechanism of 7-Hydroxymethyl Chlorophyll a Reductase. PMID:27072131
The 2.2-Angstrom resolution crystal structure of the carboxy-terminal region of ataxin-3. PMID:27047745
FreeSASA: An open source C library for solvent accessible surface area calculations. PMID:26973785
Structural investigation of the thymidine phosphorylase from Salmonella typhimurium in the unliganded state and its complexes with thymidine and uridine. PMID:26919527
First structure of archaeal branched-chain amino acid aminotransferase from Thermoproteus uzoniensis specific for L-amino acids and R-amines. PMID:26872794
Toward a detailed understanding of search trajectories in fragment assembly approaches to protein structure prediction. PMID:26799916
Structural basis for PECAM-1 homophilic binding. PMID:26702061
Resolving the ambiguity: Making sense of intrinsic disorder when PDB structures disagree. PMID:26683124
Characterizing informative sequence descriptors and predicting binding affinities of heterodimeric protein complexes. PMID:26681483
Quantitative H2S-mediated protein sulfhydration reveals metabolic reprogramming during the integrated stress response. PMID:26595448
PDB-Explorer: a web-based interactive map of the protein data bank in shape space. PMID:26493835
An amino acid code for irregular and mixed protein packing. PMID:26370334
Sequential unfolding of the hemolysin two-partner secretion domain from Proteus mirabilis. PMID:26350294
Detection of trans-cis flips and peptide-plane flips in protein structures. PMID:26249342
The 2015 Nucleic Acids Research Database Issue and molecular biology database collection. PMID:25593347
PDB_REDO: automated re-refinement of X-ray structure models in the PDB PubMed citations: 106.

106 articles citing: PDB_REDO: automated re-refinement of X-ray structure models in the PDB

Structural Bioinformatics and Deep Learning of Metalloproteins: Recent Advances and Applications. PMID:35887033
Serial macromolecular crystallography at ALBA Synchrotron Light Source. PMID:35511023
Pre- and Post-publication Verification for Reproducible Data Mining in Macromolecular Crystallography. PMID:35507266
Initial Steps to Engineer Coproheme Decarboxylase to Obtain Stereospecific Monovinyl, Monopropionyl Deuterohemes. PMID:35141216
Structure-guided stabilization of pathogen-derived peptide-HLA-E complexes using non-natural amino acids conserves native TCR recognition. PMID:35108401
Sculpting therapeutic monoclonal antibody N-glycans using endoglycosidases. PMID:34998123
Discovery of a novel pseudo β-hairpin structure of N-truncated amyloid-β for use as a vaccine against Alzheimer's disease. PMID:34776512
Improving sampling of crystallographic disorder in ensemble refinement. PMID:34726164
Structure of a Ty1 restriction factor reveals the molecular basis of transposition copy number control. PMID:34552077
A method for intuitively extracting macromolecular dynamics from structural disorder. PMID:34535675
New restraints and validation approaches for nucleic acid structures in PDB-REDO. PMID:34473084
Priming mycobacterial ESX-secreted protein B to form a channel-like structure. PMID:34337436
Structural basis for glucocorticoid receptor recognition of both unmodified and methylated binding sites, precursors of a modern recognition element. PMID:34289059
Motions around conserved helical weak spots facilitate GPCR activation. PMID:34272892
Cross-Reactive SARS-CoV-2 Neutralizing Antibodies From Deep Mining of Early Patient Responses. PMID:34211469
Structure-based phylogeny identifies avoralstat as a TMPRSS2 inhibitor that prevents SARS-CoV-2 infection in mice. PMID:33844653
Catalytic and structural properties of ATP-dependent caprolactamase from Pseudomonas jessenii. PMID:33826169
Synchrotron Radiation as a Tool for Macromolecular X-Ray Crystallography: a XXI Century Perspective. PMID:33603257
Arresting the Catalytic Arginine in Chlorite Dismutases: Impact on Heme Coordination, Thermal Stability, and Catalysis. PMID:33586945
An electron transfer competent structural ensemble of membrane-bound cytochrome P450 1A1 and cytochrome P450 oxidoreductase. PMID:33420418
CERES: a cryo-EM re-refinement system for continuous improvement of deposited models. PMID:33404525
The Convergence of the Hedgehog/Intein Fold in Different Protein Splicing Mechanisms. PMID:33171880
A Proline-Based Tectons and Supramolecular Synthons for Drug Design 2.0: A Case Study of ACEI. PMID:33114370
A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry. PMID:32857966
Structural and mechanistic analysis of ATPase inhibitors targeting mycobacterial DNA gyrase. PMID:32728686
Crystal Structures of Ternary Complexes of MEF2 and NKX2-5 Bound to DNA Reveal a Disease Related Protein-Protein Interaction Interface. PMID:32681840
Structure, Dynamics and Cellular Insight Into Novel Substrates of the Legionella pneumophila Type II Secretion System. PMID:32656228
A Review of Deep Learning Methods for Antibodies. PMID:32354020
Structural Insights into the Unique Activation Mechanisms of a Non-classical Calpain and Its Disease-Causing Variants. PMID:31968260
Structure of Drosophila melanogaster ARC1 reveals a repurposed molecule with characteristics of retroviral Gag. PMID:31911950
Structural and Functional Analyses of Human ChaC2 in Glutathione Metabolism. PMID:31878259
Facilities that make the PDB data collection more powerful. PMID:31724231
A Consensus Binding Motif for the PP4 Protein Phosphatase. PMID:31585692
Prediction of models for ordered solvent in macromolecular structures by a classifier based upon resolution-independent projections of local feature data. PMID:31373570
Sharp kinking of a coiled-coil in MutS allows DNA binding and release. PMID:31372631
Evidence for phospholipid export from the bacterial inner membrane by the Mla ABC transport system. PMID:31235958
Crystal structure of the 65-kilodalton amino-terminal fragment of DNA topoisomerase I from the gram-positive model organism Streptococcus mutans. PMID:31204053
Biophysical characterization of full-length human phenylalanine hydroxylase provides a deeper understanding of its quaternary structure equilibrium. PMID:31076506
Molecular Basis of Broad Spectrum N-Glycan Specificity and Processing of Therapeutic IgG Monoclonal Antibodies by Endoglycosidase S2. PMID:30937380
An assessment of three human methylenetetrahydrofolate dehydrogenase/cyclohydrolase-ligand complexes following further refinement. PMID:30839287
Making glycoproteins a little bit sweeter with PDB-REDO. PMID:30084395
Automatic recognition of ligands in electron density by machine learning. PMID:30016407
Cryptic glucocorticoid receptor-binding sites pervade genomic NF-κB response elements. PMID:29626214
Secreted heme peroxidase from Dictyostelium discoideum: Insights into catalysis, structure, and biological role. PMID:29242189
PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. PMID:29126160
The L33F darunavir resistance mutation acts as a molecular anchor reducing the flexibility of the HIV-1 protease 30s and 80s loops. PMID:29124158
A distance geometry-based description and validation of protein main-chain conformation. PMID:28989721
Genome-scale detection of positive selection in nine primates predicts human-virus evolutionary conflicts. PMID:28977405
Molstack-Interactive visualization tool for presentation, interpretation, and validation of macromolecules and electron density maps. PMID:28815771
Tethering not required: the glucocorticoid receptor binds directly to activator protein-1 recognition motifs to repress inflammatory genes. PMID:28591827
Structural Analysis of the Glucocorticoid Receptor Ligand-Binding Domain in Complex with Triamcinolone Acetonide and a Fragment of the Atypical Coregulator, Small Heterodimer Partner. PMID:28396564
Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding. PMID:28233410
Crystal structure and structure-based mutagenesis of actin-specific ADP-ribosylating toxin CPILE-a as novel enterotoxin. PMID:28199340
A Structural Investigation into Oct4 Regulation by Orphan Nuclear Receptors, Germ Cell Nuclear Factor (GCNF), and Liver Receptor Homolog-1 (LRH-1). PMID:27984042
A public database of macromolecular diffraction experiments. PMID:27841751
An Acrobatic Substrate Metamorphosis Reveals a Requirement for Substrate Conformational Dynamics in Trypsin Proteolysis. PMID:27810896
Validation and correction of Zn-CysxHisy complexes. PMID:27710932
Data publication with the structural biology data grid supports live analysis. PMID:26947396
Structure of human carbamoyl phosphate synthetase: deciphering the on/off switch of human ureagenesis. PMID:26592762
Structural determinants of reductive terpene cyclization in iridoid biosynthesis. PMID:26551396
Structure of a fungal form of aspartate semialdehyde dehydrogenase from Cryptococcus neoformans. PMID:26527262
Dead-End Elimination with a Polarizable Force Field Repacks PCNA Structures. PMID:26287633
Detection of trans-cis flips and peptide-plane flips in protein structures. PMID:26249342
(Patho-)physiological relevance of PINK1-dependent ubiquitin phosphorylation. PMID:26162776
Building a virtual ligand screening pipeline using free software: a survey. PMID:26094053
Ligand binding specificity of RutR, a member of the TetR family of transcription regulators in Escherichia coli. PMID:25685666
An approach to creating a more realistic working model from a protein data bank entry. PMID:25605595
High accuracy of Karplus equations for relating three-bond J couplings to protein backbone torsion angles. PMID:25511552
Phosphorylation by PINK1 releases the UBL domain and initializes the conformational opening of the E3 ubiquitin ligase Parkin. PMID:25375667
Identification and structural analysis of an L-asparaginase enzyme from guinea pig with putative tumor cell killing properties. PMID:25320094
Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data. PMID:25286839
Operation of the Australian Store.Synchrotron for macromolecular crystallography. PMID:25286837
Structure of glutathione S-transferase 1 from the major human hookworm parasite Necator americanus (Na-GST-1) in complex with glutathione. PMID:25195885
The PDB_REDO server for macromolecular structure model optimization. PMID:25075342
Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining. PMID:25075337
Structural and biochemical analyses of alanine racemase from the multidrug-resistant Clostridium difficile strain 630. PMID:25004969
Refinement of macromolecular structures against neutron data with SHELXL2013. PMID:24587788
Improved crystallographic structures using extensive combinatorial refinement. PMID:24076406
Using stable MutS dimers and tetramers to quantitatively analyze DNA mismatch recognition and sliding clamp formation. PMID:23821665
Expectation bias and information content. PMID:23385742
Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX. PMID:22868759
PDB_REDO: constructive validation, more than just looking for errors. PMID:22505269
Low-resolution refinement tools in REFMAC5. PMID:22505260
Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER. PMID:22505257
Towards automated crystallographic structure refinement with phenix.refine. PMID:22505256
Drug design for ever, from hype to hope. PMID:22252446
The good, the bad and the twisted: a survey of ligand geometry in protein crystal structures. PMID:22246295
Accessible surfaces of beta proteins increase with increasing protein molecular mass more rapidly than those of other proteins. PMID:22145047
NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB. PMID:22139937
Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank. PMID:22034521
A new generation of crystallographic validation tools for the protein data bank. PMID:22000512
X-ray crystallography: Assessment and validation of protein-small molecule complexes for drug discovery. PMID:21779303
CSAR benchmark exercise of 2010: selection of the protein-ligand complexes. PMID:21728306
Gaia: automated quality assessment of protein structure models. PMID:21700672
The role of Co²+ in the crystallization of human SENP1 and comments on the limitations of automated refinement protocols. PMID:21505236
The evolving field of imaging mass spectrometry and its impact on future biological research. PMID:21322093
On the complexity of Engh and Huber refinement restraints: the angle τ as example. PMID:21123875
A series of PDB related databases for everyday needs. PMID:21071423
GPCRDB: information system for G protein-coupled receptors. PMID:21045054
Unmet challenges of structural genomics. PMID:20810277
phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. PMID:20648263
Detection of unrealistic molecular environments in protein structures based on expected electron densities. PMID:20405167
Crystal structure of the APOBEC3G catalytic domain reveals potential oligomerization interfaces. PMID:20152150
On the use of logarithmic scales for analysis of diffraction data. PMID:19966414
4D prediction of protein (1)H chemical shifts. PMID:19876601
The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries. PMID:19809795
PDB_REDO: constructive validation, more than just looking for errors PubMed citations: 102.

102 articles citing: PDB_REDO: constructive validation, more than just looking for errors

Fine-tuning spermidine binding modes in the putrescine binding protein PotF. PMID:34801550
Cryo-EM single-particle structure refinement and map calculation using Servalcat. PMID:34605431
New restraints and validation approaches for nucleic acid structures in PDB-REDO. PMID:34473084
Structural basis of PETISCO complex assembly during piRNA biogenesis in C. elegans. PMID:34413138
'All That Glitters Is Not Gold': High-Resolution Crystal Structures of Ligand-Protein Complexes Need Not Always Represent Confident Binding Poses. PMID:34202053
FragMAXapp: crystallographic fragment-screening data-analysis and project-management system. PMID:34076593
Representations of protein structure for exploring the conformational space: A speed-accuracy trade-off. PMID:34025948
Considerations Regarding Activity Determinants of Fungal Polyphenol Oxidases Based on Mutational and Structural Studies. PMID:33741634
Synchrotron Radiation as a Tool for Macromolecular X-Ray Crystallography: a XXI Century Perspective. PMID:33603257
Detection of translational noncrystallographic symmetry in Patterson functions. PMID:33559603
LAHMA: structure analysis through local annotation of homology-matched amino acids. PMID:33404523
Phasertng: directed acyclic graphs for crystallographic phasing. PMID:33404520
Local and global analysis of macromolecular atomic displacement parameters. PMID:33021494
Iris: Interactive all-in-one graphical validation of 3D protein model iterations. PMID:32964594
Segmented flow generator for serial crystallography at the European X-ray free electron laser. PMID:32908128
Structural alphabets for conformational analysis of nucleic acids available at dnatco.datmos.org. PMID:32876056
A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry. PMID:32857966
Coarse-grained (hybrid) integrative modeling of biomolecular interactions. PMID:32514329
Computational reconstruction of atomistic protein structures from coarse-grained models. PMID:31969975
Rigid fusions of designed helical repeat binding proteins efficiently protect a binding surface from crystal contacts. PMID:31700118
Structural analysis of biological targets by host:guest crystal lattice engineering. PMID:31645583
Sequence assignment for low-resolution modelling of protein crystal structures. PMID:31373574
Structural Basis of H+-Dependent Conformational Change in a Bacterial MATE Transporter. PMID:30449688
Refining the macromolecular model - achieving the best agreement with the data from X-ray diffraction experiment. PMID:30416256
Nucleobase carbonyl groups are poor Mg2+ inner-sphere binders but excellent monovalent ion binders-a critical PDB survey. PMID:30409785
Homology-based loop modeling yields more complete crystallographic protein structures. PMID:30224962
Making glycoproteins a little bit sweeter with PDB-REDO. PMID:30084395
ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. PMID:29872003
Combination of aptamer and drug for reversible anticoagulation in cardiopulmonary bypass. PMID:29863725
Multi-position data collection and dynamic beam sizing: recent improvements to the automatic data-collection algorithms on MASSIF-1. PMID:29717714
Unravelling the specificity and mechanism of sialic acid recognition by the gut symbiont Ruminococcus gnavus. PMID:29259165
An allosteric binding site of the α7 nicotinic acetylcholine receptor revealed in a humanized acetylcholine-binding protein. PMID:29237730
Structure and activity of ChiX: a peptidoglycan hydrolase required for chitinase secretion by Serratia marcescens. PMID:29229757
Homology-based hydrogen bond information improves crystallographic structures in the PDB. PMID:29168245
Two-faced Fcab prevents polymerization with VEGF and reveals thermodynamics and the 2.15 Å crystal structure of the complex. PMID:28816592
Understanding inhibitor resistance in Mps1 kinase through novel biophysical assays and structures. PMID:28726638
Rapid cadmium SAD phasing at the standard wavelength (1 Å). PMID:28695858
Structural Basis for Specific Interaction of TGFβ Signaling Regulators SARA/Endofin with HD-PTP. PMID:28602823
Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode. PMID:28375142
Novel insights into the interaction of UBA5 with UFM1 via a UFM1-interacting sequence. PMID:28360427
The XChemExplorer graphical workflow tool for routine or large-scale protein-ligand structure determination. PMID:28291762
Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding. PMID:28233410
AceDRG: a stereochemical description generator for ligands. PMID:28177307
Validation and extraction of molecular-geometry information from small-molecule databases. PMID:28177306
Keep it together: restraints in crystallographic refinement of macromolecule-ligand complexes. PMID:28177305
Structural basis of human PCNA sliding on DNA. PMID:28071730
X-ray crystal structure of the N-terminal region of Moloney murine leukemia virus integrase and its implications for viral DNA recognition. PMID:28066922
Structure-based rationale for differential recognition of lacto- and neolacto- series glycosphingolipids by the N-terminal domain of human galectin-8. PMID:28000747
A crotonyl-CoA reductase-carboxylase independent pathway for assembly of unusual alkylmalonyl-CoA polyketide synthase extender units. PMID:28000660
Exploring the potential of boronic acids as inhibitors of OXA-24/40 β-lactamase. PMID:27997706
Mg2+ ions: do they bind to nucleobase nitrogens? PMID:27923930
A public database of macromolecular diffraction experiments. PMID:27841751
Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography. PMID:27545823
Tackling the crystallographic structure determination of the COP9 signalosome. PMID:26960120
Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations. PMID:26894674
Functional dichotomy in the 16S rRNA (m1A1408) methyltransferase family and control of catalytic activity via a novel tryptophan mediated loop reorganization. PMID:26609134
Structure of UBE2Z Enzyme Provides Functional Insight into Specificity in the FAT10 Protein Conjugation Machinery. PMID:26555268
Structural Basis for Antigenic Peptide Recognition and Processing by Endoplasmic Reticulum (ER) Aminopeptidase 2. PMID:26381406
Streptococcus pneumoniae NanC: STRUCTURAL INSIGHTS INTO THE SPECIFICITY AND MECHANISM OF A SIALIDASE THAT PRODUCES A SIALIDASE INHIBITOR. PMID:26370075
Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin. PMID:26327386
Detection of trans-cis flips and peptide-plane flips in protein structures. PMID:26249342
MutS/MutL crystal structure reveals that the MutS sliding clamp loads MutL onto DNA. PMID:26163658
A structural, functional, and computational analysis suggests pore flexibility as the base for the poor selectivity of CNG channels. PMID:26100907
Using support vector machines to improve elemental ion identification in macromolecular crystal structures. PMID:25945580
Crystal structure of the human mitochondrial chaperonin symmetrical football complex. PMID:25918392
Structural and Biochemical Analysis of Tyrosine Phosphatase Related to Biofilm Formation A (TpbA) from the Opportunistic Pathogen Pseudomonas aeruginosa PAO1. PMID:25909591
Lipidic cubic phase serial millisecond crystallography using synchrotron radiation. PMID:25866654
Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps. PMID:25760616
Models of protein-ligand crystal structures: trust, but verify. PMID:25665575
A series of PDB-related databanks for everyday needs. PMID:25352545
Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data. PMID:25286839
Aromatic aldehydes at the active site of aldehyde oxidoreductase from Desulfovibrio gigas: reactivity and molecular details of the enzyme-substrate and enzyme-product interaction. PMID:25261288
Mechanisms of neutralization of a human anti-α-toxin antibody. PMID:25210036
Structure of the N-terminal Gyrase B fragment in complex with ADP⋅Pi reveals rigid-body motion induced by ATP hydrolysis. PMID:25202966
Structure of glutathione S-transferase 1 from the major human hookworm parasite Necator americanus (Na-GST-1) in complex with glutathione. PMID:25195885
Structure of the 2,4'-dihydroxyacetophenone dioxygenase from Alcaligenes sp. 4HAP. PMID:25195757
The structure of α-haemoglobin in complex with a haemoglobin-binding domain from Staphylococcus aureus reveals the elusive α-haemoglobin dimerization interface. PMID:25084376
The PDB_REDO server for macromolecular structure model optimization. PMID:25075342
Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining. PMID:25075337
Biochemical and structural insights into microtubule perturbation by CopN from Chlamydia pneumoniae. PMID:25056950
Substrate specificities and conformational flexibility of 3-ketosteroid 9α-hydroxylases. PMID:25049233
Structural and biochemical analyses of alanine racemase from the multidrug-resistant Clostridium difficile strain 630. PMID:25004969
The structural and functional basis of catalysis mediated by NAD(P)H:acceptor Oxidoreductase (FerB) of Paracoccus denitrificans. PMID:24817153
Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package. PMID:24816093
Automated identification of elemental ions in macromolecular crystal structures. PMID:24699654
Metabolic and target-site mechanisms combine to confer strong DDT resistance in Anopheles gambiae. PMID:24675797
Ensemble refinement shows conformational flexibility in crystal structures of human complement factor D. PMID:24598742
Autotaxin: structure-function and signaling. PMID:24548887
High-resolution structure of the M14-type cytosolic carboxypeptidase from Burkholderia cenocepacia refined exploiting PDB_REDO strategies. PMID:24531462
Kinetic and structural studies of aldehyde oxidoreductase from Desulfovibrio gigas reveal a dithiolene-based chemistry for enzyme activation and inhibition by H(2)O(2). PMID:24391748
The future of crystallography in drug discovery. PMID:24372145
The quality and validation of structures from structural genomics. PMID:24203341
Crystallographic model validation: from diagnosis to healing. PMID:24064406
Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination. PMID:24034303
The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites. PMID:23895374
Quantification of free ligand conformational preferences by NMR and their relationship to the bioactive conformation. PMID:23886813
The role of structural bioinformatics resources in the era of integrative structural biology. PMID:23633580
Solvated protein-DNA docking using HADDOCK. PMID:23625455
Time passes yet errors remain: comments on the structure of N10-formyltetrahydrofolate synthetase. PMID:23533144
Expectation bias and information content. PMID:23385742
CheShift-2 resolves a local inconsistency between two X-ray crystal structures. PMID:22945426
To B or not to B: a question of resolution? PMID:22505267
Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank PubMed citations: 52.

52 articles citing: Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank

The identification and characterization of an oxalyl-CoA synthetase from grass pea (Lathyrus sativus L.). PMID:35359497
New restraints and validation approaches for nucleic acid structures in PDB-REDO. PMID:34473084
Structure of human factor VIIa-soluble tissue factor with calcium, magnesium and rubidium. PMID:34076594
FragMAXapp: crystallographic fragment-screening data-analysis and project-management system. PMID:34076593
Torpedo californica acetylcholinesterase is stabilized by binding of a divalent metal ion to a novel and versatile 4D motif. PMID:33686648
A lysozyme with altered substrate specificity facilitates prey cell exit by the periplasmic predator Bdellovibrio bacteriovorus. PMID:32968056
A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry. PMID:32857966
Two-site recognition of Staphylococcus aureus peptidoglycan by lysostaphin SH3b. PMID:31686030
Structural basis for activation of a diguanylate cyclase required for bacterial predation in Bdellovibrio. PMID:31501441
Nucleotide signaling pathway convergence in a cAMP-sensing bacterial c-di-GMP phosphodiesterase. PMID:31355487
Building and rebuilding N-glycans in protein structure models. PMID:30988258
Homology-based loop modeling yields more complete crystallographic protein structures. PMID:30224962
Inhibition of strigolactone receptors by N-phenylanthranilic acid derivatives: Structural and functional insights. PMID:29523686
Databases, Repositories, and Other Data Resources in Structural Biology. PMID:28573593
Crystal structure of U2 snRNP SF3b components: Hsh49p in complex with Cus1p-binding domain. PMID:28348170
Rational Design of Protein C Activators. PMID:28294177
The young person's guide to the PDB. PMID:28132477
Validation and correction of Zn-CysxHisy complexes. PMID:27710932
Loop Electrostatics Asymmetry Modulates the Preexisting Conformational Equilibrium in Thrombin. PMID:27347732
Interrupting peptidoglycan deacetylation during Bdellovibrio predator-prey interaction prevents ultimate destruction of prey wall, liberating bacterial-ghosts. PMID:27211869
Molprobity's ultimate rotamer-library distributions for model validation. PMID:27018641
The impact of crystallization conditions on structure-based drug design: A case study on the methylene blue/acetylcholinesterase complex. PMID:26990888
How the Linker Connecting the Two Kringles Influences Activation and Conformational Plasticity of Prothrombin. PMID:26763231
Privateer: software for the conformational validation of carbohydrate structures. PMID:26581513
Dead-End Elimination with a Polarizable Force Field Repacks PCNA Structures. PMID:26287633
A Suite of Engineered GFP Molecules for Oligomeric Scaffolding. PMID:26278175
Detection of trans-cis flips and peptide-plane flips in protein structures. PMID:26249342
Glycan complexity dictates microbial resource allocation in the large intestine. PMID:26112186
Rho GTPase Recognition by C3 Exoenzyme Based on C3-RhoA Complex Structure. PMID:26067270
Carbohydrate anomalies in the PDB. PMID:25885951
Why Ser and not Thr brokers catalysis in the trypsin fold. PMID:25664608
An approach to creating a more realistic working model from a protein data bank entry. PMID:25605595
Structural analysis of a novel small molecule ligand bound to the CXCL12 chemokine. PMID:25356720
A series of PDB-related databanks for everyday needs. PMID:25352545
Altered peptide ligands revisited: vaccine design through chemically modified HLA-A2-restricted T cell epitopes. PMID:25311806
Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data. PMID:25286839
The PDB_REDO server for macromolecular structure model optimization. PMID:25075342
Room-temperature macromolecular serial crystallography using synchrotron radiation. PMID:25075341
Anomalies in the refinement of isoleucine. PMID:24699648
High-resolution structure of the M14-type cytosolic carboxypeptidase from Burkholderia cenocepacia refined exploiting PDB_REDO strategies. PMID:24531462
The benzimidazole based drugs show good activity against T. gondii but poor activity against its proposed enoyl reductase enzyme target. PMID:24398298
Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server. PMID:24356774
Modelling three-dimensional protein structures for applications in drug design. PMID:24216321
The Geminin and Idas coiled coils preferentially form a heterodimer that inhibits Geminin function in DNA replication licensing. PMID:24064211
The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites. PMID:23895374
Assembly of a π-π stack of ligands in the binding site of an acetylcholine-binding protein. PMID:23695669
Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles? PMID:23442792
Basic mechanism of transcription by RNA polymerase II. PMID:22982365
Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX. PMID:22868759
Structural characterization of binding mode of smoking cessation drugs to nicotinic acetylcholine receptors through study of ligand complexes with acetylcholine-binding protein. PMID:22553201
PDB_REDO: constructive validation, more than just looking for errors. PMID:22505269
Drug design for ever, from hype to hope. PMID:22252446

Re-refinement from deposited X-ray data can deliver improved models for most PDB entries PubMed citations: 45.

PDB improvement starts with data deposition PubMed citations: 20.

Validation and correction of Zn-Cys x His y complexes PubMed citations: 13.

Data Mining of Macromolecular Structures PubMed citations: 6.

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structural biology
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data mining
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ModBase database of comparative protein structure models

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SWISS-MODEL Repository of 3D protein structure models

PDBsum; at-a-glance overview of macromolecular structures

Compilation and Creation of datasets from PDB

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PDB_REDO databank Names More detailed information about this field from each metasource. × PDB_REDO databank metasource: bio.tools version: extracted_at: 2022-11-04T11:32:38.349519 pdb_redo metasource: bio.tools version: extracted_at: 2022-11-04T11:32:38.349519 Close

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Worldwide Protein Data Bank

PDB-REDO

PDB facilities

ModBase database of comparative protein structure models

RCSB Protein Data Bank

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Protein Data Bank Japan

SWISS-MODEL Repository of 3D protein structure models

PDBsum; at-a-glance overview of macromolecular structures

Compilation and Creation of datasets from PDB

Protein Data Bank: Proteins, Interfaces, Structures and Assemblies

Jenalib: Jena Library of Biological Macromolecules

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Protein Data Bank in Europe

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