SUPERFAMILY
Names
More detailed information about this field from each metasource.
SUPERFAMILY
metasource: Fairsharing.org
version: FAIRsharing.org: SUPERFAMILY; SUPERFAMILY; DOI: https://doi.org/10.25504/FAIRsharing.frryvx; Last edited: April 26, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:33.505738
superfamily
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:33.505738
Names
More detailed information about this field from each metasource.
SUPERFAMILY
metasource: Fairsharing.orgversion: FAIRsharing.org: SUPERFAMILY; SUPERFAMILY; DOI: https://doi.org/10.25504/FAIRsharing.frryvx; Last edited: April 26, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:33.505738
superfamily
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:33:33.505738
Names
More detailed information about this field from each metasource.
SUPERFAMILY
metasource: Fairsharing.orgversion: FAIRsharing.org: SUPERFAMILY; SUPERFAMILY; DOI: https://doi.org/10.25504/FAIRsharing.frryvx; Last edited: April 26, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:33.505738
superfamily
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:33:33.505738
SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes.
Description
More detailed information about this field from each metasource.
SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes.
metasource: Fairsharing.orgversion: FAIRsharing.org: SUPERFAMILY; SUPERFAMILY; DOI: https://doi.org/10.25504/FAIRsharing.frryvx; Last edited: April 26, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
The SUPERFAMILY database contains a library of hidden Markov models representing all proteins of known structure. The database is based on the SCOP 'superfamily' level of protein domain classification which groups together the most distantly related proteins which have a common evolutionary ancestor. There is a public server at http://supfam.org which provides three services: sequence searching, multiple alignments to sequences of known structure, and structural assignments to all complete genomes. Given an amino acid or nucleotide query sequence the server will return the domain architecture and SCOP classification. The server produces alignments of the query sequences with sequences of known structure, and includes multiple alignments of genome and PDB sequences. The structural assignments are carried out on all complete genomes (currently 59) covering approximately half of the soluble protein domains. The assignments, superfamily breakdown, and statistics on them are available from the server. The database is currently used by this group and others for genome annotation, structural genomics, gene prediction, and domain-based genomic studies.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
It provides protein domain assignments at the structural classification of protein superfamily level for completely sequenced genomes, metagenomes and other gene collections such as UniProt. Our scoring component now uses HMMER3. A cloud-based pipeline was implemented and is publicly available. The SUPERFAMILY reference tree of life has been improved allowing the user to highlight a chosen superfamily, family or domain architecture on the tree of life.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:33:33.505738
Webpage:
http://supfam.orgWebpage
More detailed information about this field from each metasource.
http://supfam.org
metasource: Fairsharing.orgversion: FAIRsharing.org: SUPERFAMILY; SUPERFAMILY; DOI: https://doi.org/10.25504/FAIRsharing.frryvx; Last edited: April 26, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:33.505738
http://supfam.org/SUPERFAMILY/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Licence:
Name: Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0Licence name
More detailed information about this field from each metasource.
Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0
metasource: Fairsharing.orgversion: FAIRsharing.org: SUPERFAMILY; SUPERFAMILY; DOI: https://doi.org/10.25504/FAIRsharing.frryvx; Last edited: April 26, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
Licence URL
More detailed information about this field from each metasource.
http://opendatacommons.org/licenses/pddl/1.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: SUPERFAMILY; SUPERFAMILY; DOI: https://doi.org/10.25504/FAIRsharing.frryvx; Last edited: April 26, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
Publications:
(6)
Publications
More detailed information about this field from each metasource.
Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
PMID: 11697912
metasource: Fairsharing.org
version: FAIRsharing.org: SUPERFAMILY; SUPERFAMILY; DOI: https://doi.org/10.25504/FAIRsharing.frryvx; Last edited: April 26, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny
PMID: 19036790
metasource: Fairsharing.org
version: FAIRsharing.org: SUPERFAMILY; SUPERFAMILY; DOI: https://doi.org/10.25504/FAIRsharing.frryvx; Last edited: April 26, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
The SUPERFAMILY database in 2007: families and functions
PMID: 17098927
metasource: Fairsharing.org
version: FAIRsharing.org: SUPERFAMILY; SUPERFAMILY; DOI: https://doi.org/10.25504/FAIRsharing.frryvx; Last edited: April 26, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
SUPERFAMILY 1.75 including a domain-centric gene ontology method
PMID: 21062816
metasource: Fairsharing.org
version: FAIRsharing.org: SUPERFAMILY; SUPERFAMILY; DOI: https://doi.org/10.25504/FAIRsharing.frryvx; Last edited: April 26, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:33.505738
The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver
PMID: 30445555
metasource: Fairsharing.org
version: FAIRsharing.org: SUPERFAMILY; SUPERFAMILY; DOI: https://doi.org/10.25504/FAIRsharing.frryvx; Last edited: April 26, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://dx.doi.org/10.1093/nar/gku1041
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
PMID: 11697912
metasource: Fairsharing.org
version: FAIRsharing.org: SUPERFAMILY; SUPERFAMILY; DOI: https://doi.org/10.25504/FAIRsharing.frryvx; Last edited: April 26, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny
PMID: 19036790
metasource: Fairsharing.org
version: FAIRsharing.org: SUPERFAMILY; SUPERFAMILY; DOI: https://doi.org/10.25504/FAIRsharing.frryvx; Last edited: April 26, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
The SUPERFAMILY database in 2007: families and functions
PMID: 17098927
metasource: Fairsharing.org
version: FAIRsharing.org: SUPERFAMILY; SUPERFAMILY; DOI: https://doi.org/10.25504/FAIRsharing.frryvx; Last edited: April 26, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
SUPERFAMILY 1.75 including a domain-centric gene ontology method
PMID: 21062816
metasource: Fairsharing.org
version: FAIRsharing.org: SUPERFAMILY; SUPERFAMILY; DOI: https://doi.org/10.25504/FAIRsharing.frryvx; Last edited: April 26, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:33.505738
The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver
PMID: 30445555
metasource: Fairsharing.org
version: FAIRsharing.org: SUPERFAMILY; SUPERFAMILY; DOI: https://doi.org/10.25504/FAIRsharing.frryvx; Last edited: April 26, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://dx.doi.org/10.1093/nar/gku1041
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
PubMed citations: 519.
519 articles citing: Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
In Silico Identification and Characterization of a Hypothetical Protein From Rhodobacter capsulatus Revealing S-Adenosylmethionine-Dependent Methyltransferase Activity. PMID:35478993
The Plant Invertase/Pectin Methylesterase Inhibitor Superfamily. PMID:35401607
Hypothetical protein predicted to be tumor suppressor: a protein functional analysis. PMID:35399005
Investigating the Functional Role of Hypothetical Proteins From an Antarctic Bacterium Pseudomonas sp. Lz4W: Emphasis on Identifying Proteins Involved in Cold Adaptation. PMID:35360867
Quantifying and Cataloguing Unknown Sequences within Human Microbiomes. PMID:35258340
Sequence Divergence and Functional Specializations of the Ancient Spliceosomal SF3b: Implications in Flexibility and Adaptations of the Multi-Protein Complex. PMID:35082828
Systematic analysis of HD-ZIP transcription factors in sesame genome and gene expression profiling of SiHD-ZIP class I entailing drought stress responses at early seedling stage. PMID:34993726
Characterization of a Secretory YML079-like Cupin Protein That Contributes to Sclerotinia sclerotiorum Pathogenicity. PMID:34946121
Identification of potential inhibitory analogs of metastasis tumor antigens (MTAs) using bioactive compounds: revealing therapeutic option to prevent malignancy. PMID:34743299
Genomic Insights Into the Archaea Inhabiting an Australian Radioactive Legacy Site. PMID:34737728
RefPlantNLR is a comprehensive collection of experimentally validated plant disease resistance proteins from the NLR family. PMID:34669691
Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo. PMID:34428301
RNA polymerases in strict endosymbiont bacteria with extreme genome reduction show distinct erosions that might result in limited and differential promoter recognition. PMID:34324516
Nonrefoldability is Pervasive Across the E. coli Proteome. PMID:34308638
Bioinformatic Analysis of the Campylobacter jejuni Type VI Secretion System and Effector Prediction. PMID:34276628
Genome-wide association study of signature genetic alterations among pseudomonas aeruginosa cystic fibrosis isolates. PMID:34161396
Schistosomiasis Drug Discovery in the Era of Automation and Artificial Intelligence. PMID:34135888
Nucleoporin TPR Affects C2C12 Myogenic Differentiation via Regulation of Myh4 Expression. PMID:34063931
DOE JGI Metagenome Workflow. PMID:34006627
The Chaperonin GroESL Facilitates Caulobacter crescentus Cell Division by Supporting the Functions of the Z-Ring Regulators FtsA and FzlA. PMID:33947758
Signatures of conserved and unique molecular features in Afrotheria. PMID:33441654
The N-terminal region of Jaw1 has a role to inhibit the formation of organized smooth endoplasmic reticulum as an intrinsically disordered region. PMID:33436890
DeepTFactor: A deep learning-based tool for the prediction of transcription factors. PMID:33372147
An Educational Bioinformatics Project to Improve Genome Annotation. PMID:33365016
Integrated Co-functional Network Analysis on the Resistance and Virulence Features in Acinetobacter baumannii. PMID:33224132
In silico functional prediction of hypothetical proteins from the core genome of Corynebacterium pseudotuberculosis biovar ovis. PMID:32913672
In silico Functional Annotation and Characterization of Hypothetical Proteins from Serratia marcescens FGI94. PMID:32834707
Effector Repertoire of Phytophthora betacei: In Search of Possible Virulence Factors Responsible for Its Host Specificity. PMID:32582295
Functional and Structural Analysis of Predicted Proteins Obtained from Homo sapiens' Minisatellite 33.15-Tagged Transcript pAKT-45 Variants. PMID:32566673
The TERB1-TERB2-MAJIN complex of mouse meiotic telomeres dates back to the common ancestor of metazoans. PMID:32408858
An inventory of interactors of the human HSP60/HSP10 chaperonin in the mitochondrial matrix space. PMID:32060690
Bacterial Origin and Reductive Evolution of the CPR Group. PMID:32031619
Antimicrobial Activity of Protein Fraction from Naja ashei Venom Against Staphylococcus epidermidis. PMID:31936872
The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures. PMID:31724711
The mixed liver and heart transcriptome dataset of the New Zealand brushtail possum, Trichosurus vulpecula. PMID:31700950
The draft genome of Actinia tenebrosa reveals insights into toxin evolution. PMID:31641475
Protein Abundance Biases the Amino Acid Composition of Disordered Regions to Minimize Non-functional Interactions. PMID:31442477
Structural Basis of the Subcellular Topology Landscape of Escherichia coli. PMID:31404336
Nascent Polypeptide Domain Topology and Elongation Rate Direct the Cotranslational Hierarchy of Hsp70 and TRiC/CCT. PMID:31400849
Comparative genomic analysis suggests that the sperm-specific sodium/proton exchanger and soluble adenylyl cyclase are key regulators of CatSper among the Metazoa. PMID:31372239
Short- and Long-Term Effects of UVA on Arabidopsis Are Mediated by a Novel cGMP Phosphodiesterase. PMID:31353185
Fold combinations in multi-domain proteins. PMID:31249437
Genetic variant pathogenicity prediction trained using disease-specific clinical sequencing data sets. PMID:31235655
Protein Structure-Guided Hidden Markov Models (HMMs) as A Powerful Method in the Detection of Ancestral Endogenous Viral Elements. PMID:30986983
Comparative Genomics Between Saccharomyces kudriavzevii and S. cerevisiae Applied to Identify Mechanisms Involved in Adaptation. PMID:30930934
Differential proteostatic regulation of insoluble and abundant proteins. PMID:30903148
Testing Empirical Support for Evolutionary Models that Root the Tree of Life. PMID:30887086
Draft genomic and transcriptome resources for marine chelicerate Tachypleus tridentatus. PMID:30806641
MultiDomainBenchmark: a multi-domain query and subject database suite. PMID:30764761
PDZ Domains Across the Microbial World: Molecular Link to the Proteases, Stress Response, and Protein Synthesis. PMID:30698789
Multivariate Information Fusion With Fast Kernel Learning to Kernel Ridge Regression in Predicting LncRNA-Protein Interactions. PMID:30697228
Genome structure and evolution of Antirrhinum majus L. PMID:30692677
ACCBN: ant-Colony-clustering-based bipartite network method for predicting long non-coding RNA-protein interactions. PMID:30626319
Functional Prediction of Hypothetical Proteins from Shigella flexneri and Validation of the Predicted Models by Using ROC Curve Analysis. PMID:30602087
Rab5 GTPases are required for optimal TORC2 function. PMID:30578283
Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes. PMID:30538677
SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions. PMID:30533006
Comprehensive Transcriptional Profiling of the Gastrointestinal Tract of Ruminants from Birth to Adulthood Reveals Strong Developmental Stage Specific Gene Expression. PMID:30530642
Genome-wide analysis reveals the evolution and structural features of WRINKLED1 in plants. PMID:30446819
The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver. PMID:30445555
New insights into the evolution and functional divergence of the SWEET family in Saccharum based on comparative genomics. PMID:30404601
A de Novo EDA-Variant in a Litter of Shorthaired Standard Dachshunds with X-Linked Hypohidrotic Ectodermal Dysplasia. PMID:30397018
What is an archaeon and are the Archaea really unique? PMID:30357005
Towards region-specific propagation of protein functions. PMID:30304483
A gene-rich fraction analysis of the Passiflora edulis genome reveals highly conserved microsyntenic regions with two related Malpighiales species. PMID:30158558
The mechanism by which a distinguishing arabinofuranosidase can cope with internal di-substitutions in arabinoxylans. PMID:30127853
Homology Inference Based on a Reconciliation Approach for the Comparative Genomics of Protozoa. PMID:30034216
De novo profile generation based on sequence context specificity with the long short-term memory network. PMID:30021530
Methods for Physical Characterization of Phase-Separated Bodies and Membrane-less Organelles. PMID:30017918
Cancer-predicting transcriptomic and epigenetic signatures revealed for ulcerative colitis in patient-derived epithelial organoids. PMID:29983891
Functional annotation of hypothetical proteins from the Exiguobacterium antarcticum strain B7 reveals proteins involved in adaptation to extreme environments, including high arsenic resistance. PMID:29940001
GeneMANIA update 2018. PMID:29912392
Comprehensive analysis of Verticillium nonalfalfae in silico secretome uncovers putative effector proteins expressed during hop invasion. PMID:29894496
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
Improved strategy for the curation and classification of kinases, with broad applicability to other eukaryotic protein groups. PMID:29717207
Positive and Negative Regulation of Angiogenesis by Soluble Vascular Endothelial Growth Factor Receptor-1. PMID:29702562
Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species. PMID:29700415
Organization of feed-forward loop motifs reveals architectural principles in natural and engineered networks. PMID:29670941
Characterizing Phage Genomes for Therapeutic Applications. PMID:29642590
HMMER Cut-off Threshold Tool (HMMERCTTER): Supervised classification of superfamily protein sequences with a reliable cut-off threshold. PMID:29579071
Homology modeling and epitope prediction of Der f 33. PMID:29561952
Identification of the S-transferase like superfamily bacillithiol transferases encoded by Bacillus subtilis. PMID:29451913
Mutations in CFAP43 and CFAP44 cause male infertility and flagellum defects in Trypanosoma and human. PMID:29449551
Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome. PMID:29434576
Do Viruses Exchange Genes across Superkingdoms of Life? PMID:29163404
Severe Fertility Effects of sheepish Sperm Caused by Failure To Enter Female Sperm Storage Organs in Drosophila melanogaster. PMID:29158336
Genome-wide identification and characterization of cacao WRKY transcription factors and analysis of their expression in response to witches' broom disease. PMID:29084273
Forecasting residue-residue contact prediction accuracy. PMID:29036497
Potential and pitfalls in the genetic diagnosis of kidney diseases. PMID:28980668
Compositional and expression analyses of the glideosome during the Plasmodium life cycle reveal an additional myosin light chain required for maximum motility. PMID:28893907
Autoantibody Repertoire in APECED Patients Targets Two Distinct Subgroups of Proteins. PMID:28861084
The Enigmatic Origin of Papillomavirus Protein Domains. PMID:28832519
Tum1 is involved in the metabolism of sterol esters in Saccharomyces cerevisiae. PMID:28830344
Conserved Transcriptional Responses to Nutrient Stress in Bloom-Forming Algae. PMID:28769884
Diversity and distribution of nuclease bacteriocins in bacterial genomes revealed using Hidden Markov Models. PMID:28715501
Transcription Factor Repertoire of Necrotrophic Fungal Phytopathogen Ascochyta rabiei: Predominance of MYB Transcription Factors As Potential Regulators of Secretome. PMID:28659964
Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum YT. PMID:28623373
Family-specific scaling laws in bacterial genomes. PMID:28605556
Simple adjustment of the sequence weight algorithm remarkably enhances PSI-BLAST performance. PMID:28578660
Recognition of a structural domain (RWDBD) in Gcn1 proteins that interacts with the RWD domain containing proteins. PMID:28526057
Cilia- and Flagella-Associated Protein 69 Regulates Olfactory Transduction Kinetics in Mice. PMID:28495971
AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking. PMID:28424069
Functional and biochemical characterization of a T cell-associated anti-apoptotic protein, GIMAP6. PMID:28381553
Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification. PMID:28344575
The H3 loop of antibodies shows unique structural characteristics. PMID:28342222
Revised domain structure of ulvan lyase and characterization of the first ulvan binding domain. PMID:28327560
Structure-based function analysis of putative conserved proteins with isomerase activity from Haemophilus influenzae. PMID:28324524
Structure-based functional annotation of putative conserved proteins having lyase activity from Haemophilus influenzae. PMID:28324295
Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions. PMID:28280526
A New Reference Genome Assembly for the Microcrustacean Daphnia pulex. PMID:28235826
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
From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer. PMID:28066816
Arguments Reinforcing the Three-Domain View of Diversified Cellular Life. PMID:28050162
An expressed, endogenous Nodavirus-like element captured by a retrotransposon in the genome of the plant parasitic nematode Bursaphelenchus xylophilus. PMID:28004836
Mapping the membrane proteome of anaerobic gut fungi identifies a wealth of carbohydrate binding proteins and transporters. PMID:27998268
A Subset of Ubiquitin-Conjugating Enzymes Is Essential for Plant Immunity. PMID:27909045
In vivo protein interaction network analysis reveals porin-localized antibiotic inactivation in Acinetobacter baumannii strain AB5075. PMID:27834373
The Transcriptome of Exophiala dermatitidis during Ex-vivo Skin Model Infection. PMID:27822460
Protein social behavior makes a stronger signal for partner identification than surface geometry. PMID:27802579
In Silico Analysis of Glutaminase from Different Species of Escherichia and Bacillus. PMID:27582590
Evidence for the sexual origin of heterokaryosis in arbuscular mycorrhizal fungi. PMID:27572831
Cel5I, a SLH-Containing Glycoside Hydrolase: Characterization and Investigation on Its Role in Ruminiclostridium cellulolyticum. PMID:27501457
Did Viruses Evolve As a Distinct Supergroup from Common Ancestors of Cells? PMID:27497315
S18 family of mitochondrial ribosomal proteins: evolutionary history and Gly132 polymorphism in colon carcinoma. PMID:27489352
Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence. PMID:27472895
Two hAT transposon genes were transferred from Brassicaceae to broomrapes and are actively expressed in some recipients. PMID:27452947
Analyses of Compact Trichinella Kinomes Reveal a MOS-Like Protein Kinase with a Unique N-Terminal Domain. PMID:27412987
Evolution of the Calcium-Based Intracellular Signaling System. PMID:27358427
The Ensembl gene annotation system. PMID:27337980
Comparative Protein Structure Modeling Using MODELLER. PMID:27322406
De novo assembly of a tadpole shrimp (Triops newberryi) transcriptome and preliminary differential gene expression analysis. PMID:27292122
Benchmarking the next generation of homology inference tools. PMID:27256311
Genomic analysis of Ugandan and Rwandan chicken ecotypes using a 600 k genotyping array. PMID:27230772
MOCAT2: a metagenomic assembly, annotation and profiling framework. PMID:27153620
Hologenome analysis of two marine sponges with different microbiomes. PMID:26926518
Homology modeling and assigned functional annotation of an uncharacterized antitoxin protein from Streptomyces xinghaiensis. PMID:26912949
The effector candidate repertoire of the arbuscular mycorrhizal fungus Rhizophagus clarus. PMID:26861502
Homology-Based Prediction of Potential Protein-Protein Interactions between Human Erythrocytes and Plasmodium falciparum. PMID:26740742
Why do Sequence Signatures Predict Enzyme Mechanism? Homology versus Chemistry. PMID:26740739
The TIM Barrel Architecture Facilitated the Early Evolution of Protein-Mediated Metabolism. PMID:26733481
The Haemonchus contortus kinome--a resource for fundamental molecular investigations and drug discovery. PMID:26644012
Quantitative differential proteomics of yeast extracellular matrix: there is more to it than meets the eye. PMID:26608260
A phylogenomic data-driven exploration of viral origins and evolution. PMID:26601271
A bioinformatics insight to rhizobial globins: gene identification and mapping, polypeptide sequence and phenetic analysis, and protein modeling. PMID:26594329
Draft Genome Sequence of the Fungus Trametes hirsuta 072. PMID:26586872
Evolution of the EKA family of powdery mildew avirulence-effector genes from the ORF 1 of a LINE retrotransposon. PMID:26556056
Activity Augmentation of Amphioxus Peptidoglycan Recognition Protein BbtPGRP3 via Fusion with a Chitin Binding Domain. PMID:26479246
Following the Footsteps of Chlamydial Gene Regulation. PMID:26424812
Biomimetics: From Bioinformatics to Rational Design of Dendrimers as Gene Carriers. PMID:26382062
Selection of recombinant anti-SH3 domain antibodies by high-throughput phage display. PMID:26332758
The value of protein structure classification information-Surveying the scientific literature. PMID:26313554
The Evolution of the Secreted Regulatory Protein Progranulin. PMID:26248158
Mitochondrial genomes are retained by selective constraints on protein targeting. PMID:26195779
The mouse wellhaarig (we) mutations result from defects in epidermal-type transglutaminase 3 (Tgm3). PMID:26194162
Defining the Domain Arrangement of the Mammalian Target of Rapamycin Complex Component Rictor Protein. PMID:26176550
Predictive and comparative analysis of Ebolavirus proteins. PMID:26158395
SInCRe-structural interactome computational resource for Mycobacterium tuberculosis. PMID:26130660
Expansion and Functional Divergence of Jumonji C-Containing Histone Demethylases: Significance of Duplications in Ancestral Angiosperms and Vertebrates. PMID:26059336
Large-Scale Evolutionary Analysis of Genes and Supergene Clusters from Terpenoid Modular Pathways Provides Insights into Metabolic Diversification in Flowering Plants. PMID:26046541
Draft Genome Sequence of Sporidiobolus salmonicolor CBS 6832, a Red-Pigmented Basidiomycetous Yeast. PMID:25999568
Function-selective domain architecture plasticity potentials in eukaryotic genome evolution. PMID:25980317
Comparative transcriptome profiling approach to glean virulence and immunomodulation-related genes of Fasciola hepatica. PMID:25956885
Staphylococcus aureus Survives with a Minimal Peptidoglycan Synthesis Machine but Sacrifices Virulence and Antibiotic Resistance. PMID:25951442
Splice junctions are constrained by protein disorder. PMID:25934802
Long non-coding RNA discovery across the genus anopheles reveals conserved secondary structures within and beyond the Gambiae complex. PMID:25903279
Solution structure of a soluble fragment derived from a membrane protein by shotgun proteolysis. PMID:25877662
Crystal structure of Helicobacter pylori pseudaminic acid biosynthesis N-acetyltransferase PseH: implications for substrate specificity and catalysis. PMID:25781966
The ribosome challenge to the RNA world. PMID:25739364
Structural prediction of a novel laminarinase from the psychrophilic Glaciozyma antarctica PI12 and its temperature adaptation analysis. PMID:25721655
The evaluation of tools used to predict the impact of missense variants is hindered by two types of circularity. PMID:25684150
Tandem-repeat protein domains across the tree of life. PMID:25653910
xiNET: cross-link network maps with residue resolution. PMID:25648531
A novel transposable Mu-like prophage in Bacillus alcalophilus CGMCC 1.3604 (ATCC 27647). PMID:25628219
Rab5-family guanine nucleotide exchange factors bind retromer and promote its recruitment to endosomes. PMID:25609093
Evolutionary patterns in coiled-coils. PMID:25577198
Transcriptome-wide analysis of SAMe superfamily to novelty phosphoethanolamine N-methyltransferase copy in Lonicera japonica. PMID:25551601
Overview of computational vaccinology: vaccine development through information technology. PMID:25534541
The SUPERFAMILY 1.75 database in 2014: a doubling of data. PMID:25414345
Pre-metazoan origins and evolution of the cadherin adhesome. PMID:25395670
Acanthamoeba castellanii STAT protein. PMID:25338074
Genome-wide identification and tissue-specific expression analysis of UDP-glycosyltransferases genes confirm their abundance in Cicer arietinum (Chickpea) genome. PMID:25290312
Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. PMID:25204769
Cloning, purification and preliminary crystallographic analysis of the Helicobacter pylori pseudaminic acid biosynthesis N-acetyltransferase PseH. PMID:25195909
Bioinformatic indications that COPI- and clathrin-based transport systems are not present in chloroplasts: an Arabidopsis model. PMID:25137124
De novo assembly of Aureococcus anophagefferens transcriptomes reveals diverse responses to the low nutrient and low light conditions present during blooms. PMID:25104951
Cyclic di-GMP-dependent signaling pathways in the pathogenic Firmicute Listeria monocytogenes. PMID:25101646
Modeling sequence and function similarity between proteins for protein functional annotation. PMID:25101328
General mechanism of two-state protein folding kinetics. PMID:25056406
Nme family of proteins--clues from simple animals. PMID:25042404
De novo transcriptomes of a mixotrophic and a heterotrophic ciliate from marine plankton. PMID:24983246
Evolution of the ribosome at atomic resolution. PMID:24982194
Ranking non-synonymous single nucleotide polymorphisms based on disease concepts. PMID:24980617
Comparative transcriptome analysis of four prymnesiophyte algae. PMID:24926657
In Silico Prediction of T and B Cell Epitopes of Der f 25 in Dermatophagoides farinae. PMID:24895543
From sequence to enzyme mechanism using multi-label machine learning. PMID:24885296
Hemoglobins in the genome of the cryptomonad Guillardia theta. PMID:24885221
Protein flexibility facilitates quaternary structure assembly and evolution. PMID:24866000
An allosteric switch for pro-HGF/Met signaling using zymogen activator peptides. PMID:24859116
Structural and functional analysis of a novel psychrophilic β-mannanase from Glaciozyma antarctica PI12. PMID:24849507
Think globally and solve locally: secondary memory-based network learning for automated multi-species function prediction. PMID:24843788
Classification of intrinsically disordered regions and proteins. PMID:24773235
Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms. PMID:24710297
Ankyrin domains across the Tree of Life. PMID:24688847
In silico characterization of an atypical MAPK phosphatase of Plasmodium falciparum as a suitable target for drug discovery. PMID:24605883
Benchmarking of methods for genomic taxonomy. PMID:24574292
Global patterns of protein domain gain and loss in superkingdoms. PMID:24499935
Comparative analysis of proteomes and functionomes provides insights into origins of cellular diversification. PMID:24492748
BuT2 is a member of the third major group of hAT transposons and is involved in horizontal transfer events in the genus Drosophila. PMID:24459285
Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20. PMID:24391926
MMDB and VAST+: tracking structural similarities between macromolecular complexes. PMID:24319143
SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures. PMID:24304899
Revisiting amino acid substitution matrices for identifying distantly related proteins. PMID:24281694
The Structure-Function Linkage Database. PMID:24271399
Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis. PMID:24270792
Exploring fold space preferences of new-born and ancient protein superfamilies. PMID:24244135
Enzyme reaction annotation using cloud techniques. PMID:24222895
PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool. PMID:24219505
Comparative transcriptome analysis of geographically distinct virulent and attenuated Babesia bovis strains reveals similar gene expression changes through attenuation. PMID:24195453
Comparative analysis of barophily-related amino acid content in protein domains of Pyrococcus abyssi and Pyrococcus furiosus. PMID:24187517
mRNA-Seq and microarray development for the Grooved Carpet shell clam, Ruditapes decussatus: a functional approach to unravel host-parasite interaction. PMID:24168212
The diversity of zinc-finger genes on human chromosome 19 provides an evolutionary mechanism for defense against inherited endogenous retroviruses. PMID:24162661
Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility. PMID:23991065
Masculinization of gene expression is associated with exaggeration of male sexual dimorphism. PMID:23966876
A network of HMG-box transcription factors regulates sexual cycle in the fungus Podospora anserina. PMID:23935511
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
Characterization of a serine hydrolase targeted by acyl-protein thioesterase inhibitors in Toxoplasma gondii. PMID:23913689
Link clustering reveals structural characteristics and biological contexts in signed molecular networks. PMID:23826198
Variant surface antigens of malaria parasites: functional and evolutionary insights from comparative gene family classification and analysis. PMID:23805789
A daily-updated tree of (sequenced) life as a reference for genome research. PMID:23778980
A method for WD40 repeat detection and secondary structure prediction. PMID:23776530
Genomics-guided analysis of NAD recycling yields functional elucidation of COG1058 as a new family of pyrophosphatases. PMID:23776507
Transcriptomic analysis of Ustilago maydis infecting Arabidopsis reveals important aspects of the fungus pathogenic mechanisms. PMID:23733054
Sequence and structural investigation of a novel psychrophilic α-amylase from Glaciozyma antarctica PI12 for cold-adaptation analysis. PMID:23686283
Developmental gene discovery in a hemimetabolous insect: de novo assembly and annotation of a transcriptome for the cricket Gryllus bimaculatus. PMID:23671567
Reconstituting protein interaction networks using parameter-dependent domain-domain interactions. PMID:23651452
Predicting the functional consequences of cancer-associated amino acid substitutions. PMID:23620363
The challenge of increasing Pfam coverage of the human proteome. PMID:23603847
Protein complexes are under evolutionary selection to assemble via ordered pathways. PMID:23582331
Computational interaction analysis of organophosphorus pesticides with different metabolic proteins in humans. PMID:23554709
Viral evolution: Primordial cellular origins and late adaptation to parasitism. PMID:23550145
Structural phylogenomics reveals gradual evolutionary replacement of abiotic chemistries by protein enzymes in purine metabolism. PMID:23516625
A domain-centric solution to functional genomics via dcGO Predictor. PMID:23514627
Competition sensing: the social side of bacterial stress responses. PMID:23456045
IGSF9 family proteins. PMID:23417431
Genomic and secretomic analyses reveal unique features of the lignocellulolytic enzyme system of Penicillium decumbens. PMID:23383313
Evolutionary optimization of protein folding. PMID:23341762
ccm2-like is required for cardiovascular development as a novel component of the Heg-CCM pathway. PMID:23328253
Trypanosome CNOT10 is essential for the integrity of the NOT deadenylase complex and for degradation of many mRNAs. PMID:23221646
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. PMID:23203986
D²P²: database of disordered protein predictions. PMID:23203878
ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species. PMID:23180770
DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. PMID:23161684
Functional characterization of a tomato COBRA-like gene functioning in fruit development and ripening. PMID:23140186
Hybrid sequencing approach applied to human fecal metagenomic clone libraries revealed clones with potential biotechnological applications. PMID:23082187
Identification of positive selection in disease response genes within members of the Poaceae. PMID:23073005
The transcriptome profile of the mosquito Culex quinquefasciatus following permethrin selection. PMID:23071746
Structure of RdxA--an oxygen-insensitive nitroreductase essential for metronidazole activation in Helicobacter pylori. PMID:23039228
Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. PMID:23033316
Tools to kill: genome of one of the most destructive plant pathogenic fungi Macrophomina phaseolina. PMID:22992219
Structure of the Archaeoglobus fulgidus orphan ORF AF1382 determined by sulfur SAD from a moderately diffracting crystal. PMID:22948926
Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya. PMID:22920653
Distribution and prediction of catalytic domains in 2-oxoglutarate dependent dioxygenases. PMID:22862831
The purification of the Chlamydomonas reinhardtii chloroplast ClpP complex: additional subunits and structural features. PMID:22772861
Structural prediction of a novel chitinase from the psychrophilic Glaciozyma antarctica PI12 and an analysis of its structural properties and function. PMID:22710891
Respiratory membrane endo-hydrogenase activity in the microaerophile Azorhizobium caulinodans is bidirectional. PMID:22662125
3D profile-based approach to proteome-wide discovery of novel human chemokines. PMID:22586462
Characterization of tannase protein sequences of bacteria and fungi: an in silico study. PMID:22460647
Ribosomal history reveals origins of modern protein synthesis. PMID:22427882
A phylogenetic analysis of the globins in fungi. PMID:22384087
Pleiotropic roles of a ribosomal protein in Dictyostelium discoideum. PMID:22363460
Target selection for structural genomics based on combining fold recognition and crystallisation prediction methods: application to the human proteome. PMID:22354707
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
A model of genetic search for beneficial mutations: estimating the constructive capacities of mutagenesis. PMID:22212997
Evolution and functional diversification of the small heat shock protein/α-crystallin family in higher plants. PMID:22210597
The phylogenomic roots of modern biochemistry: origins of proteins, cofactors and protein biosynthesis. PMID:22210458
Androglobin: a chimeric globin in metazoans that is preferentially expressed in Mammalian testes. PMID:22115833
Crystallization and preliminary X-ray analysis of the Entamoeba histolytica α-actinin-2 rod domain. PMID:22102030
Origins and evolution of the HET-s prion-forming protein: searching for other amyloid-forming solenoids. PMID:22096554
The quantitative proteome of a human cell line. PMID:22068332
IDEAL: Intrinsically Disordered proteins with Extensive Annotations and Literature. PMID:22067451
Probable presence of an ubiquitous cryptic mitochondrial gene on the antisense strand of the cytochrome oxidase I gene. PMID:22024028
Identification of Plasmodium vivax proteins with potential role in invasion using sequence redundancy reduction and profile hidden Markov models. PMID:21984903
Selection in coastal Synechococcus (cyanobacteria) populations evaluated from environmental metagenomes. PMID:21931665
Characterization of the small RNA transcriptome of the diatom, Thalassiosira pseudonana. PMID:21857960
The Vein Patterning 1 (VEP1) gene family laterally spread through an ecological network. PMID:21818306
siRNA knockdown of ribosomal protein gene RPL19 abrogates the aggressive phenotype of human prostate cancer. PMID:21799931
Lafora disease E3-ubiquitin ligase malin is related to TRIM32 at both the phylogenetic and functional level. PMID:21798009
A novel Lawsonia intracellularis autotransporter protein is a prominent antigen. PMID:21697340
Binary classification of protein molecules into intrinsically disordered and ordered segments. PMID:21693062
Molecular cloning, tissue distribution and ontogenetic expression of Xiang pig chemerin and its involvement in regulating energy metabolism through Akt and ERK1/2 signaling pathways. PMID:21643960
A network of SCOP hidden Markov models and its analysis. PMID:21635719
The proteomic complexity and rise of the primordial ancestor of diversified life. PMID:21612591
A bioinformatics classifier and database for heme-copper oxygen reductases. PMID:21559461
A systems biology approach for the investigation of the heparin/heparan sulfate interactome. PMID:21454685
A discriminative method for family-based protein remote homology detection that combines inductive logic programming and propositional models. PMID:21429187
HMMerThread: detecting remote, functional conserved domains in entire genomes by combining relaxed sequence-database searches with fold recognition. PMID:21423752
Assembling a protein-protein interaction map of the SSU processome from existing datasets. PMID:21423703
Analysis of osmotin, a PR protein as metabolic modulator in plants. PMID:21383921
OsBC1L4 encodes a COBRA-like protein that affects cellulose synthesis in rice. PMID:21264494
The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence. PMID:21192786
Cholera- and anthrax-like toxins are among several new ADP-ribosyltransferases. PMID:21170356
A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae. PMID:21119626
Molecular evolution and selection patterns of plant F-box proteins with C-terminal kelch repeats. PMID:21119043
In silico gene expression analysis in Codonopsis lanceolata root. PMID:21088900
Proteome evolution and the metabolic origins of translation and cellular life. PMID:21082171
Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans. PMID:21080964
SUPERFAMILY 1.75 including a domain-centric gene ontology method. PMID:21062816
A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1. PMID:20959003
Evidences for increased expression variation of duplicate genes in budding yeast: from cis- to trans-regulation effects. PMID:20935054
Prototypes of elementary functional loops unravel evolutionary connections between protein functions. PMID:20823313
Genomic repertoires of DNA-binding transcription factors across the tree of life. PMID:20675356
Part I: characterization of the extracellular proteome of the extreme thermophile Caldicellulosiruptor saccharolyticus by GeLC-MS2. PMID:20623222
Part II: defining and quantifying individual and co-cultured intracellular proteomes of two thermophilic microorganisms by GeLC-MS2 and spectral counting. PMID:20582400
Two components of a velvet-like complex control hyphal morphogenesis, conidiophore development, and penicillin biosynthesis in Penicillium chrysogenum. PMID:20543063
Cell surface display of chimeric glycoproteins via the S-layer of Paenibacillus alvei. PMID:20513375
History of biological metal utilization inferred through phylogenomic analysis of protein structures. PMID:20498051
PhenoFam-gene set enrichment analysis through protein structural information. PMID:20478033
Computational protein design: validation and possible relevance as a tool for homology searching and fold recognition. PMID:20463972
Widespread head-to-head hydrocarbon biosynthesis in bacteria and role of OleA. PMID:20418421
Role of vimA in cell surface biogenesis in Porphyromonas gingivalis. PMID:20378652
TAT-pathway-dependent lipoproteins as a niche-based adaptation in prokaryotes. PMID:20333370
AlgK is a TPR-containing protein and the periplasmic component of a novel exopolysaccharide secretin. PMID:20159471
Transposon identification using profile HMMs. PMID:20158867
TreeVector: scalable, interactive, phylogenetic trees for the web. PMID:20126613
Identification of recurring protein structure microenvironments and discovery of novel functional sites around CYS residues. PMID:20122268
SoyDB: a knowledge database of soybean transcription factors. PMID:20082720
The Zur regulon of Corynebacterium glutamicum ATCC 13032. PMID:20055984
Quality measures for protein alignment benchmarks. PMID:20047958
Predicting gene function using hierarchical multi-label decision tree ensembles. PMID:20044933
Comprehensive in silico prediction and analysis of chlamydial outer membrane proteins reflects evolution and life style of the Chlamydiae. PMID:20040079
Generation and gene ontology based analysis of expressed sequence tags (EST) from a Panax ginseng C. A. Meyer roots. PMID:19943115
A statistical model of protein sequence similarity and function similarity reveals overly-specific function predictions. PMID:19844580
Significant speedup of database searches with HMMs by search space reduction with PSSM family models. PMID:19828575
Evolutionary descent of prion genes from the ZIP family of metal ion transporters. PMID:19784368
Role of the transcriptional regulator RamB (Rv0465c) in the control of the glyoxylate cycle in Mycobacterium tuberculosis. PMID:19767422
Does negative auto-regulation increase gene duplicability? PMID:19664220
Tandem and cryptic amino acid repeats accumulate in disordered regions of proteins. PMID:19486509
Crystal structure of histidine phosphotransfer protein ShpA, an essential regulator of stalk biogenesis in Caulobacter crescentus. PMID:19450606
Recognition of double strand breaks by a mutator protein (MU2) in Drosophila melanogaster. PMID:19424425
webPRC: the Profile Comparer for alignment-based searching of public domain databases. PMID:19420063
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
Assembly and transport mechanism of tripartite drug efflux systems. PMID:19289182
Crystal structure of YfeU protein from Haemophilus influenzae: a predicted etherase involved in peptidoglycan recycling. PMID:19234762
Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. PMID:19219566
Protein domain organisation: adding order. PMID:19178743
Improved homology-driven computational validation of protein-protein interactions motivated by the evolutionary gene duplication and divergence hypothesis. PMID:19152684
Differentiating protein-coding and noncoding RNA: challenges and ambiguities. PMID:19043537
Genome and proteome annotation: organization, interpretation and integration. PMID:19019817
Genome-wide survey of prokaryotic serine proteases: analysis of distribution and domain architectures of five serine protease families in prokaryotes. PMID:19019219
AS-ALPS: a database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse. PMID:19015123
Protein subfamily assignment using the Conserved Domain Database. PMID:19014584
Profile Comparer: a program for scoring and aligning profile hidden Markov models. PMID:18845584
Patterns of evolutionary constraints on genes in humans. PMID:18840274
NetGrep: fast network schema searches in interactomes. PMID:18801179
Comparative analysis of function and interaction of transcription factors in nematodes: extensive conservation of orthology coupled to rapid sequence evolution. PMID:18752680
A protein domain-based interactome network for C. elegans early embryogenesis. PMID:18692475
Validating annotations for uncharacterized proteins in Shewanella oneidensis. PMID:18687039
The cadherin superfamily in Anopheles gambiae: a comparative study with Drosophila melanogaster. PMID:18629193
Specialized hidden markov model databases for microbial genomics. PMID:18629132
Architectures and functional coverage of protein-protein interfaces. PMID:18620705
The effectiveness of position- and composition-specific gap costs for protein similarity searches. PMID:18586708
The hidden universal distribution of amino acid biosynthetic networks: a genomic perspective on their origins and evolution. PMID:18541022
A structural annotation resource for the selection of putative target proteins in the malaria parasite. PMID:18500983
Yeast Pgc1p (YPL206c) controls the amount of phosphatidylglycerol via a phospholipase C-type degradation mechanism. PMID:18434318
Comparative protein structure modeling using Modeller. PMID:18428767
Rethinking proteasome evolution: two novel bacterial proteasomes. PMID:18389302
Evolution of exceptionally large genes in prokaryotes. PMID:18322635
The maize (Zea mays L.) roothairless3 gene encodes a putative GPI-anchored, monocot-specific, COBRA-like protein that significantly affects grain yield. PMID:18298667
Analysis of the human kinome using methods including fold recognition reveals two novel kinases. PMID:18270584
Comparative secretome analysis suggests low plant cell wall degrading capacity in Frankia symbionts. PMID:18226217
Using likelihood-free inference to compare evolutionary dynamics of the protein networks of H. pylori and P. falciparum. PMID:18052538
Gene3D: comprehensive structural and functional annotation of genomes. PMID:18032434
Modeling protein network evolution under genome duplication and domain shuffling. PMID:17999763
Improving model construction of profile HMMs for remote homology detection through structural alignment. PMID:17999748
Determinants of protein function revealed by combinatorial entropy optimization. PMID:17976239
Wide diversity in structure and expression profiles among members of the Caenorhabditis elegans globin protein family. PMID:17916248
Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world. PMID:17908824
Molecular evolution of the MAGUK family in metazoan genomes. PMID:17678554
Crystal structure of an acetyltransferase protein from Vibrio cholerae strain N16961. PMID:17623843
Integration of rotation and piston motions in coiled-coil signal transduction. PMID:17573470
Identification of regions critically affecting kinetics and allosteric regulation of the Escherichia coli ADP-glucose pyrophosphorylase by modeling and pentapeptide-scanning mutagenesis. PMID:17496097
fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies. PMID:17485476
cTFbase: a database for comparative genomics of transcription factors in cyanobacteria. PMID:17439663
The innate immune repertoire in cnidaria--ancestral complexity and stochastic gene loss. PMID:17437634
HMM-ModE--improved classification using profile hidden Markov models by optimising the discrimination threshold and modifying emission probabilities with negative training sequences. PMID:17389042
Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PMID:17373854
Hierarchy and feedback in the evolution of the Escherichia coli transcription network. PMID:17372223
Structural and functional diversity of the microbial kinome. PMID:17355172
Matrix Metalloproteinase-9 (MMP-9) polymorphisms in patients with cutaneous malignant melanoma. PMID:17346338
Plasmids and rickettsial evolution: insight from Rickettsia felis. PMID:17342200
Yeast two-hybrid map of Arabidopsis TFIID. PMID:17340043
A network perspective on the evolution of metabolism by gene duplication. PMID:17326820
Glycolipid transfer proteins. PMID:17320476
Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance. PMID:17254327
Using phylogeny to improve genome-wide distant homology recognition. PMID:17238281
New developments in the InterPro database. PMID:17202162
ERp57 is essential for efficient folding of glycoproteins sharing common structural domains. PMID:17170699
POGs/PlantRBP: a resource for comparative genomics in plants. PMID:17142226
ForestTreeDB: a database dedicated to the mining of tree transcriptomes. PMID:17130142
Structure of Arabidopsis thaliana At1g77540 protein, a minimal acetyltransferase from the COG2388 family. PMID:17128971
The liganding of glycolipid transfer protein is controlled by glycolipid acyl structure. PMID:17105344
The SUPERFAMILY database in 2007: families and functions. PMID:17098927
Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry. PMID:17098870
TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method. PMID:17065464
Mining the Arabidopsis thaliana genome for highly-divergent seven transmembrane receptors. PMID:17064408
A framework for protein structure classification and identification of novel protein structures. PMID:17042958
Identification of a gene negatively affecting antibiotic production and morphological differentiation in Streptomyces coelicolor A3(2). PMID:17041057
Coding limits on the number of transcription factors. PMID:16984633
PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification. PMID:16973001
Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction. PMID:16970830
Genomic scale sub-family assignment of protein domains. PMID:16877569
AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. PMID:16855290
Chromosome-wide identification of novel imprinted genes using microarrays and uniparental disomies. PMID:16855283
MANET: tracing evolution of protein architecture in metabolic networks. PMID:16854231
A global topology map of the Saccharomyces cerevisiae membrane proteome. PMID:16847258
Evolution of +1 programmed frameshifting signals and frameshift-regulating tRNAs in the order Saccharomycetales. PMID:16838213
Sequence analysis and organization of the Neodiprion abietis nucleopolyhedrovirus genome. PMID:16809301
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
Statistical limits to the identification of ion channel domains by sequence similarity. PMID:16735758
Protein family expansions and biological complexity. PMID:16733546
Genomic patterns of pathogen evolution revealed by comparison of Burkholderia pseudomallei, the causative agent of melioidosis, to avirulent Burkholderia thailandensis. PMID:16725056
Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific gram-positive bacteria. PMID:16723015
Distinguishing protein-coding from non-coding RNAs through support vector machines. PMID:16683024
Genome of crocodilepox virus. PMID:16641289
A tale of two ferredoxins: sequence similarity and structural differences. PMID:16603087
Conservation of intrinsic disorder in protein domains and families: I. A database of conserved predicted disordered regions. PMID:16602695
A phylogenomic profile of globins. PMID:16600051
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
Protein interaction networks in plants. PMID:16575597
Structural proteomics of minimal organisms: conservation of protein fold usage and evolutionary implications. PMID:16566839
A TFIIB-like protein is indispensable for spliced leader RNA gene transcription in Trypanosoma brucei. PMID:16554554
Identification of similar regions of protein structures using integrated sequence and structure analysis tools. PMID:16526955
Exploiting protein structure data to explore the evolution of protein function and biological complexity. PMID:16524831
Structure and mechanism of an ADP-glucose phosphorylase from Arabidopsis thaliana. PMID:16519510
The structure at 2.5 A resolution of human basophilic leukemia-expressed protein BLES03. PMID:16511166
The structure at 2.4 A resolution of the protein from gene locus At3g21360, a putative Fe(II)/2-oxoglutarate-dependent enzyme from Arabidopsis thaliana. PMID:16511070
A gold standard set of mechanistically diverse enzyme superfamilies. PMID:16507141
Structure and mechanism of mouse cysteine dioxygenase. PMID:16492780
On single and multiple models of protein families for the detection of remote sequence relationships. PMID:16448555
The Epc-N domain: a predicted protein-protein interaction domain found in select chromatin associated proteins. PMID:16412250
MaGe: a microbial genome annotation system supported by synteny results. PMID:16407324
Phytome: a platform for plant comparative genomics. PMID:16381967
Channel formation by CarO, the carbapenem resistance-associated outer membrane protein of Acinetobacter baumannii. PMID:16304148
Identification of the rctA gene, which is required for repression of conjugative transfer of rhizobial symbiotic megaplasmids. PMID:16237017
Natural history of S-adenosylmethionine-binding proteins. PMID:16225687
Sequence variation in ligand binding sites in proteins. PMID:16194281
New genes from old: redeployment of dUTPase by herpesviruses. PMID:16188990
Dynamic covariation between gene expression and proteome characteristics. PMID:16131395
Functional coverage of the human genome by existing structures, structural genomics targets, and homology models. PMID:16118666
Evolution of a microbial nitrilase gene family: a comparative and environmental genomics study. PMID:16083508
Three globin lineages belonging to two structural classes in genomes from the three kingdoms of life. PMID:16061809
De novo RNA synthesis and homology modeling of the classical swine fever virus RNA polymerase. PMID:16022897
A sequence sub-sampling algorithm increases the power to detect distant homologues. PMID:16006623
The MicrobesOnline Web site for comparative genomics. PMID:15998914
Improved membrane protein topology prediction by domain assignments. PMID:15987901
The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite. PMID:15984913
InterProScan: protein domains identifier. PMID:15980438
Constitutive signal transduction by mutant Ssy5p and Ptr3p components of the SPS amino acid sensor system in Saccharomyces cerevisiae. PMID:15947203
Structural similarity to bridge sequence space: finding new families on the bridges. PMID:15840833
Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER. PMID:15831105
Practical lessons from protein structure prediction. PMID:15805122
Prediction of a common structural scaffold for proteasome lid, COP9-signalosome and eIF3 complexes. PMID:15790418
Caspases. Regulating death since the origin of life. PMID:15761210
Gene fusions and gene duplications: relevance to genomic annotation and functional analysis. PMID:15757509
Novel activator of mannose-specific phosphotransferase system permease expression in Listeria innocua, identified by screening for pediocin AcH resistance. PMID:15746330
Prokaryotic phylogenies inferred from protein structural domains. PMID:15741510
Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. PMID:15684069
Predicted hexameric structure of the Agrobacterium VirB4 C terminus suggests VirB4 acts as a docking site during type IV secretion. PMID:15668378
Phylogeny determined by protein domain content. PMID:15630082
The UCSC Proteome Browser. PMID:15608236
The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. PMID:15608188
The Universal Protein Resource (UniProt). PMID:15608167
Analysis of the S-locus structure in Prunus armeniaca L. Identification of S-haplotype specific S-RNase and F-box genes. PMID:15604734
4SCOPmap: automated assignment of protein structures to evolutionary superfamilies. PMID:15598351
C-terminal nsP1a protein of human astrovirus colocalizes with the endoplasmic reticulum and viral RNA. PMID:15564473
Molecular analysis of the CRINKLY4 gene family in Arabidopsis thaliana. PMID:15549374
Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. PMID:15523666
Components of coated vesicles and nuclear pore complexes share a common molecular architecture. PMID:15523559
Conservation of adjacency as evidence of paralogous operons. PMID:15477389
Comparative structural modeling and inference of conserved protein classes in Drosophila seminal fluid. PMID:15345744
A complementary bioinformatics approach to identify potential plant cell wall glycosyltransferase-encoding genes. PMID:15333752
Tissue-specific modification of gld-2 mRNA in C. elegans: likely C-to-U editing. PMID:15317977
Sequence-based prediction of protein domains. PMID:15240828
The anthracnose resistance locus Co-4 of common bean is located on chromosome 3 and contains putative disease resistance-related genes. PMID:15221144
Structural characterization of genomes by large scale sequence-structure threading. PMID:15061866
PASS2: an automated database of protein alignments organised as structural superfamilies. PMID:15059245
Mammalian N-acetylglutamate synthase. PMID:15050968
HIV-1 Tat directly binds to NFkappaB enhancer sequence: role in viral and cellular gene expression. PMID:14981150
GeneDB: a resource for prokaryotic and eukaryotic organisms. PMID:14681429
3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes. PMID:14681404
The SUPERFAMILY database in 2004: additions and improvements. PMID:14681402
SCOP database in 2004: refinements integrate structure and sequence family data. PMID:14681400
UniProt: the Universal Protein knowledgebase. PMID:14681372
Multi-domain protein families and domain pairs: comparison with known structures and a random model of domain recombination. PMID:14649290
PCAS--a precomputed proteome annotation database resource. PMID:14594458
Visualisation and graph-theoretic analysis of a large-scale protein structural interactome. PMID:14531933
Significance of conservative asparagine residues in the thermal hysteresis activity of carrot antifreeze protein. PMID:14531728
Functional map and domain structure of MET, the product of the c-met protooncogene and receptor for hepatocyte growth factor/scatter factor. PMID:14528000
META-PP: single interface to crucial prediction servers. PMID:12824314
Development and evaluation of an automated annotation pipeline and cDNA annotation system. PMID:12819153
The mouse secretome: functional classification of the proteins secreted into the extracellular environment. PMID:12819133
Comprehensive analysis of the mouse metabolome based on the transcriptome. PMID:12819132
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
Conservation of structure and function among tyrosine recombinases: homology-based modeling of the lambda integrase core-binding domain. PMID:12560475
The repertoire of protein kinases encoded in the draft version of the human genome: atypical variations and uncommon domain combinations. PMID:12537555
The esterase and PHD domains in CR1-like non-LTR retrotransposons. PMID:12519904
Structural characterization of the human proteome. PMID:12421749
The COBRA family of putative GPI-anchored proteins in Arabidopsis. A new fellowship in expansion. PMID:12376623
A comparison of profile hidden Markov model procedures for remote homology detection. PMID:12364612
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
Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database. PMID:11875040
The Spin/Ssty repeat: a new motif identified in proteins involved in vertebrate development from gamete to embryo. PMID:11806826
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 -
SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny
PubMed citations: 202.
202 articles citing: SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny
A chromosome-level genome assembly and intestinal transcriptome of Trypoxylus dichotomus (Coleoptera: Scarabaeidae) to understand its lignocellulose digestion ability. PMID:35764601
Prediction and expression analysis of deleterious nonsynonymous SNPs of Arabidopsis ACD11 gene by combining computational algorithms and molecular docking approach. PMID:35709304
Alternative splicing diversifies the transcriptome and proteome of the rice blast fungus during host infection. PMID:35311472
Chromosomal-Level Genome Assembly of the Springtail Tomocerus qinae (Collembola: Tomoceridae). PMID:35298623
Bulinus truncatus transcriptome - a resource to enable molecular studies of snail and schistosome biology. PMID:35284899
Chromosome-Level Genome Assembly of Anthidium xuezhongi Niu & Zhu, 2020 (Hymenoptera: Apoidea: Megachilidae: Anthidiini). PMID:35150256
A Chromosome-Level Genome Assembly of the Parasitic Wasp Chelonus formosanus Sonan 1932 (Hymenoptera: Braconidae). PMID:35104339
Evolution of host-microbe cell adherence by receptor domain shuffling. PMID:35076392
Chromosome-Level Genome Assembly of Nephotettix cincticeps (Uhler, 1896) (Hemiptera: Cicadellidae: Deltocephalinae). PMID:34677607
The first chromosome-level genome assembly of a green lacewing Chrysopa pallens and its implication for biological control. PMID:34549894
Diverse ATPase Proteins in Mobilomes Constitute a Large Potential Sink for Prokaryotic Host ATP. PMID:34305853
Comparative genome and transcriptome analyses reveal innate differences in response to host plants by two color forms of the two-spotted spider mite Tetranychus urticae. PMID:34301178
Beyond PKA: Evolutionary and structural insights that define a docking and dimerization domain superfamily. PMID:34256050
Structural and functional characterization of a plant alpha-actinin. PMID:34110107
Evolution of networks of protein domain organization. PMID:34103558
Tracing Evolution Through Protein Structures: Nature Captured in a Few Thousand Folds. PMID:34041266
A Chromosome-Level Genome Assembly of Ephestia elutella (Hübner, 1796) (Lepidoptera: Pyralidae). PMID:34014321
Characterization of the Bubblegum acyl-CoA synthetase of Microchloropsis gaditana. PMID:33793914
A chromosome-level genome of the spider Trichonephila antipodiana reveals the genetic basis of its polyphagy and evidence of an ancient whole-genome duplication event. PMID:33739402
Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation. PMID:33711918
Study on cocoonase, sericin, and degumming of silk cocoon: computational and experimental. PMID:33594479
A Highly Contiguous Genome Assembly of a Polyphagous Predatory Mite Stratiolaelaps scimitus (Womersley) (Acari: Laelapidae). PMID:33528489
A Draft Genome Assembly of Culex pipiens pallens (Diptera: Culicidae) Using PacBio Sequencing. PMID:33501937
Computing Cellulase Kinetics with a Two-Domain Linear Interaction Energy Approach. PMID:33490814
Ribosome occupancy profiles are conserved between structurally and evolutionarily related yeast domains. PMID:33483722
RUNX1/RUNX1T1 mediates alternative splicing and reorganises the transcriptional landscape in leukemia. PMID:33483506
Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity. PMID:33323129
On the emergence of P-Loop NTPase and Rossmann enzymes from a Beta-Alpha-Beta ancestral fragment. PMID:33295875
Fibrillarin evolution through the Tree of Life: Comparative genomics and microsynteny network analyses provide new insights into the evolutionary history of Fibrillarin. PMID:33075080
Transcriptomic Analysis of the Early Strobilar Development of Echinococcus granulosus. PMID:32545493
The First Draft Genome of the Plasterer Bee Colletes gigas (Hymenoptera: Colletidae: Colletes). PMID:32386319
Similar genomic patterns of clinical infective endocarditis and oral isolates of Streptococcus sanguinis and Streptococcus gordonii. PMID:32066773
The modular nature of protein evolution: domain rearrangement rates across eukaryotic life. PMID:32059645
Bacterial Origin and Reductive Evolution of the CPR Group. PMID:32031619
Bioinformatics for Renal and Urinary Proteomics: Call for Aggrandization. PMID:32024005
Biophysical prediction of protein-peptide interactions and signaling networks using machine learning. PMID:31907444
New Insights into Multistep-Phosphorelay (MSP)/ Two-Component System (TCS) Regulation: Are Plants and Bacteria that Different? PMID:31835810
Whole genome sequence and de novo assembly revealed genomic architecture of Indian Mithun (Bos frontalis). PMID:31357931
In-silico Prediction of Synergistic Anti-Cancer Drug Combinations Using Multi-omics Data. PMID:31222109
Deciphering the three-domain architecture in schlafens and the structures and roles of human schlafen12 and serpinB12 in transcriptional regulation. PMID:31026779
Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome. PMID:30904393
Global biochemical and structural analysis of the type IV pilus from the Gram-positive bacterium Streptococcus sanguinis. PMID:30837269
A High-quality Draft Genome Assembly of Sinella curviseta: A Soil Model Organism (Collembola). PMID:30668671
The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver. PMID:30445555
Organic Particles: Heterogeneous Hubs for Microbial Interactions in Aquatic Ecosystems. PMID:30416497
Draft genome sequence of Bacillus amyloliquefaciens subsp. plantarum strain Fito_F321, an endophyte microorganism from Vitis vinifera with biocontrol potential. PMID:30410642
RNA uridylation and decay in plants. PMID:30397100
Contributions of substitutions and indels to the structural variations in ancient protein superfamilies. PMID:30355304
Dissecting the Repertoire of DNA-Binding Transcription Factors of the Archaeon Pyrococcus furiosus DSM 3638. PMID:30248960
A comprehensive manually-curated compendium of bovine transcription factors. PMID:30213987
The genome sequence of the soft-rot fungus Penicillium purpurogenum reveals a high gene dosage for lignocellulolytic enzymes. PMID:30123662
Functional Prediction of Hypothetical Transcription Factors of Escherichia coli K-12 Based on Expression Data. PMID:30050664
Direction of flagellum beat propagation is controlled by proximal/distal outer dynein arm asymmetry. PMID:30030284
A Pathogen-Responsive Leucine Rich Receptor Like Kinase Contributes to Fusarium Resistance in Cereals. PMID:29997638
Comprehensive analysis of Verticillium nonalfalfae in silico secretome uncovers putative effector proteins expressed during hop invasion. PMID:29894496
Identifying differentially expressed proteins in sorghum cell cultures exposed to osmotic stress. PMID:29875393
Transcriptomics insights into the genetic regulation of root apical meristem exhaustion and determinate primary root growth in Pachycereus pringlei (Cactaceae). PMID:29867103
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
A Computational Approach Using Bioinformatics to Screening Drug Targets for Leishmania infantum Species. PMID:29785196
Abundance, diversity and domain architecture variability in prokaryotic DNA-binding transcription factors. PMID:29614096
Mutations in CFAP43 and CFAP44 cause male infertility and flagellum defects in Trypanosoma and human. PMID:29449551
Prolonged Expression of a Putative Invertase Inhibitor in Micropylar Endosperm Suppressed Embryo Growth in Arabidopsis. PMID:29441087
Identification of the Autochaperone Domain in the Type Va Secretion System (T5aSS): Prevalent Feature of Autotransporters with a β-Helical Passenger. PMID:29375499
Alpha-actinin of the chlorarchiniophyte Bigelowiella natans. PMID:29372122
Small Myristoylated Protein-3, Identified as a Potential Virulence Factor in Leishmania amazonensis, Proves to be a Protective Antigen against Visceral Leishmaniasis. PMID:29301342
Structural and functional annotation of hypothetical proteins of human adenovirus: prioritizing the novel drug targets. PMID:29212526
The genome draft of coconut (Cocos nucifera). PMID:29048487
Conformational dynamics are a key factor in signaling mediated by the receiver domain of a sensor histidine kinase from Arabidopsis thaliana. PMID:28860196
Functional Analogy in Human Metabolism: Enzymes with Different Biological Roles or Functional Redundancy? PMID:28854631
An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences. PMID:28777078
ProtozoaDB 2.0: A Trypanosoma Brucei Case Study. PMID:28726736
Tracing the Repertoire of Promiscuous Enzymes along the Metabolic Pathways in Archaeal Organisms. PMID:28703743
Coping with living in the soil: the genome of the parthenogenetic springtail Folsomia candida. PMID:28659179
Recognition of a structural domain (RWDBD) in Gcn1 proteins that interacts with the RWD domain containing proteins. PMID:28526057
Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom. PMID:28429538
Killing by Type VI secretion drives genetic phase separation and correlates with increased cooperation. PMID:28165005
Protein Bioinformatics Databases and Resources. PMID:28150231
Evaluation of a hypothetical protein for serodiagnosis and as a potential marker for post-treatment serological evaluation of tegumentary leishmaniasis patients. PMID:28150041
The evolution of function within the Nudix homology clan. PMID:27936487
The SWISS-MODEL Repository-new features and functionality. PMID:27899672
The Human Phenotype Ontology in 2017. PMID:27899602
Tailor-made transcriptional biosensors for optimizing microbial cell factories. PMID:27837353
Protein Translation Enzyme lysyl-tRNA Synthetase Presents a New Target for Drug Development against Causative Agents of Loiasis and Schistosomiasis. PMID:27806050
Structural and functional characterisation of a class I endochitinase of the carnivorous sundew (Drosera rotundifolia L.). PMID:27761648
Sex Change in Clownfish: Molecular Insights from Transcriptome Analysis. PMID:27748421
Systematic functional analysis of kinases in the fungal pathogen Cryptococcus neoformans. PMID:27677328
Evolution of Protein Domain Repeats in Metazoa. PMID:27671125
Genome-wide survey and phylogeny of S-Ribosylhomocysteinase (LuxS) enzyme in bacterial genomes. PMID:27650568
The role of ADP-ribosylation in regulating DNA interstrand crosslink repair. PMID:27587838
Evolution of the Calcium-Based Intracellular Signaling System. PMID:27358427
Whole genome sequencing as a tool for phylogenetic analysis of clinical strains of Mitis group streptococci. PMID:27325438
Gene Family Evolution Reflects Adaptation to Soil Environmental Stressors in the Genome of the Collembolan Orchesella cincta. PMID:27289101
Consensus protein design. PMID:27274091
Transcription of Sialic Acid Catabolism Genes in Corynebacterium glutamicum Is Subject to Catabolite Repression and Control by the Transcriptional Repressor NanR. PMID:27274030
UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB. PMID:27153729
Evolutionary relationships between heme-binding ferredoxin α + β barrels. PMID:27089923
Characterisation of Schizosaccharomyces pombe α-actinin. PMID:27069798
Inside the Pan-genome - Methods and Software Overview. PMID:27006628
PolyQ 2.0: an improved version of PolyQ, a database of human polyglutamine proteins. PMID:26980520
Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation. PMID:26876183
ApoCanD: Database of human apoptotic proteins in the context of cancer. PMID:26861916
Structural and functional attributes of malaria parasite diadenosine tetraphosphate hydrolase. PMID:26829485
dbEM: A database of epigenetic modifiers curated from cancerous and normal genomes. PMID:26777304
Core Promoter Plasticity Between Maize Tissues and Genotypes Contrasts with Predominance of Sharp Transcription Initiation Sites. PMID:26628745
Genomics of the Genus Bifidobacterium Reveals Species-Specific Adaptation to the Glycan-Rich Gut Environment. PMID:26590291
Beyond the E-Value: Stratified Statistics for Protein Domain Prediction. PMID:26575353
σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough. PMID:26555820
Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut. PMID:26506949
The language of the protein universe. PMID:26451980
Phylogeny of Echinoderm Hemoglobins. PMID:26247465
The Genome of Winter Moth (Operophtera brumata) Provides a Genomic Perspective on Sexual Dimorphism and Phenology. PMID:26227816
Calcium affinity of human α-actinin 1. PMID:26020004
Function-selective domain architecture plasticity potentials in eukaryotic genome evolution. PMID:25980317
Genome-wide identification and evolution of HECT genes in soybean. PMID:25894222
Homozygous MED25 mutation implicated in eye-intellectual disability syndrome. PMID:25792360
Clustering of two genes putatively involved in cyanate detoxification evolved recently and independently in multiple fungal lineages. PMID:25663439
Tandem-repeat protein domains across the tree of life. PMID:25653910
From discovery to function: the expanding roles of long noncoding RNAs in physiology and disease. PMID:25426780
The SUPERFAMILY 1.75 database in 2014: a doubling of data. PMID:25414345
A census of human RNA-binding proteins. PMID:25365966
WDSPdb: a database for WD40-repeat proteins. PMID:25348404
The Comparative Genomics and Phylogenomics of Leishmania amazonensis Parasite. PMID:25336895
Complete genome sequence of the Radiation-Resistant bacterium Rubrobacter radiotolerans RSPS-4. PMID:25197483
Entropy-driven partitioning of the hierarchical protein space. PMID:25161256
Increasing and decreasing the ultrastability of bacterial chemotaxis core signaling complexes by modifying protein-protein contacts. PMID:25119814
Cooperative secretions facilitate host range expansion in bacteria. PMID:25091146
Protein flexibility facilitates quaternary structure assembly and evolution. PMID:24866000
Cross-species gene-family fluctuations reveal the dynamics of horizontal transfers. PMID:24829449
Evolution and quantitative comparison of genome-wide protein domain distributions. PMID:24710298
Ankyrin domains across the Tree of Life. PMID:24688847
Genomics and bioinformatics resources for translational science in Rosaceae. PMID:24634697
RNA binding protein-mediated post-transcriptional gene regulation in medulloblastoma. PMID:24608801
HMPAS: Human Membrane Protein Analysis System. PMID:24564858
Global patterns of protein domain gain and loss in superkingdoms. PMID:24499935
Citrus sinensis annotation project (CAP): a comprehensive database for sweet orange genome. PMID:24489955
Finding the missing honey bee genes: lessons learned from a genome upgrade. PMID:24479613
SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures. PMID:24304899
RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria. PMID:24175918
Increments and duplication events of enzymes and transcription factors influence metabolic and regulatory diversity in prokaryotes. PMID:23922780
A thermoacidophile-specific protein family, DUF3211, functions as a fatty acid carrier with novel binding mode. PMID:23836863
Variant surface antigens of malaria parasites: functional and evolutionary insights from comparative gene family classification and analysis. PMID:23805789
Structural and functional characterization of Pseudomonas aeruginosa AlgX: role of AlgX in alginate acetylation. PMID:23779107
A method for WD40 repeat detection and secondary structure prediction. PMID:23776530
Transcription profile of soybean-root-knot nematode interaction reveals a key role of phythormones in the resistance reaction. PMID:23663436
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
A genomic signature and the identification of new sporulation genes. PMID:23396918
The repertoires of ubiquitinating and deubiquitinating enzymes in eukaryotic genomes. PMID:23393154
A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels. PMID:23390605
The plant ontology as a tool for comparative plant anatomy and genomic analyses. PMID:23220694
DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. PMID:23161684
The genome of the obligate intracellular parasite Trachipleistophora hominis: new insights into microsporidian genome dynamics and reductive evolution. PMID:23133373
MESSA: MEta-Server for protein Sequence Analysis. PMID:23031578
Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya. PMID:22920653
GFam: a platform for automatic annotation of gene families. PMID:22790981
MuSiC: identifying mutational significance in cancer genomes. PMID:22759861
Genome and proteome analysis of 7-7-1, a flagellotropic phage infecting Agrobacterium sp H13-3. PMID:22650361
Oral spirochetes implicated in dental diseases are widespread in normal human subjects and carry extremely diverse integron gene cassettes. PMID:22635997
Crystallization of a novel metal-containing cupin from Acidobacterium sp. and preliminary diffraction data analysis. PMID:22505418
Uneven spread of cis- and trans-editing aminoacyl-tRNA synthetase domains within translational compartments of P. falciparum. PMID:22355703
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
The phylogenomic roots of modern biochemistry: origins of proteins, cofactors and protein biosynthesis. PMID:22210458
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis. PMID:22139938
Proteins: form and function. PMID:22095055
Thousands of rab GTPases for the cell biologist. PMID:22022256
Evolution of vacuolar proton pyrophosphatase domains and volutin granules: clues into the early evolutionary origin of the acidocalcisome. PMID:21974828
Lafora disease E3-ubiquitin ligase malin is related to TRIM32 at both the phylogenetic and functional level. PMID:21798009
The InterPro BioMart: federated query and web service access to the InterPro Resource. PMID:21785143
Fluorescence lifetime imaging unravels C. trachomatis metabolism and its crosstalk with the host cell. PMID:21779161
AlignHUSH: alignment of HMMs using structure and hydrophobicity information. PMID:21729312
The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences. PMID:21646335
The proteomic complexity and rise of the primordial ancestor of diversified life. PMID:21612591
Constructing de novo biosynthetic pathways for chemical synthesis inside living cells. PMID:21591680
Using context to improve protein domain identification. PMID:21453511
HMMerThread: detecting remote, functional conserved domains in entire genomes by combining relaxed sequence-database searches with fold recognition. PMID:21423752
Disease and phenotype data at Ensembl. PMID:21400687
CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality. PMID:21071393
SUPERFAMILY 1.75 including a domain-centric gene ontology method. PMID:21062816
Characterization of cyanate metabolism in marine Synechococcus and Prochlorococcus spp. PMID:21057026
The impact of gene expression regulation on evolution of extracellular signaling pathways. PMID:20935258
Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line. PMID:20739923
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
Lineage-specific expansion of DNA-binding transcription factor families. PMID:20675012
Crystallization and preliminary crystallographic analysis of the central domain of Drosophila Dribble, a protein that is essential for ribosome biogenesis. PMID:20445256
Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution. PMID:20433725
From evidence to inference: probing the evolution of protein interaction networks. PMID:20357887
TAT-pathway-dependent lipoproteins as a niche-based adaptation in prokaryotes. PMID:20333370
Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function. PMID:20333304
The overlap of small molecule and protein binding sites within families of protein structures. PMID:20140189
An ontology-based search engine for protein-protein interactions. PMID:20122195
From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase. PMID:20043185
A genomic glimpse of aminoacyl-tRNA synthetases in malaria parasite Plasmodium falciparum. PMID:20042123
The evolutionary history of protein domains viewed by species phylogeny. PMID:20041107
GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains. PMID:19923231
Gene3D: merging structure and function for a Thousand genomes. PMID:19906693
Origin and evolution of the Notch signalling pathway: an overview from eukaryotic genomes. PMID:19825158
Bioinformatics and structural characterization of a hypothetical protein from Streptococcus mutans: implication of antibiotic resistance. PMID:19798411
Structural and functional constraints in the evolution of protein families. PMID:19756040
A Novel extracytoplasmic function (ECF) sigma factor regulates virulence in Pseudomonas aeruginosa. PMID:19730690
Alignment of multiple protein structures based on sequence and structure features. PMID:19587024 -
The SUPERFAMILY database in 2007: families and functions
PubMed citations: 105.
105 articles citing: The SUPERFAMILY database in 2007: families and functions
In-Silico Functional Annotation of Plasmodium falciparum Hypothetical Proteins to Identify Novel Drug Targets. PMID:35444689
Knowledge-Based Unfolded State Model for Protein Design. PMID:35298824
Structural and Functional Elucidation of IF-3 Protein of Chloroflexus aurantiacus Involved in Protein Biosynthesis: An In Silico Approach. PMID:34307671
The Origin and Evolution of Antistasin-like Proteins in Leeches (Hirudinida, Clitellata). PMID:33527140
An Alveolata secretory machinery adapted to parasite host cell invasion. PMID:33495622
In-depth transcriptome reveals the potential biotechnological application of Bothrops jararaca venom gland. PMID:33149734
Molecular characterization and functional annotation of a hypothetical protein (SCO0618) of Streptomyces coelicolor A3(2). PMID:33017872
A physics-based energy function allows the computational redesign of a PDZ domain. PMID:32636412
Questing functions and structures of hypothetical proteins from Campylobacter jejuni: a computer-aided approach. PMID:32458979
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
Immediate Effects of Ammonia Shock on Transcription and Composition of a Biogas Reactor Microbiome. PMID:31555248
Machine learning-based chemical binding similarity using evolutionary relationships of target genes. PMID:31504818
Structural Basis of the Subcellular Topology Landscape of Escherichia coli. PMID:31404336
The project MinE databrowser: bringing large-scale whole-genome sequencing in ALS to researchers and the public. PMID:31280677
Glycyrrhetinic acid binds to the conserved P-loop region and interferes with the interaction of RAS-effector proteins. PMID:30976491
A Phospholipase C-Like Protein From Ricinus communis Increases Hydroxy Fatty Acids Accumulation in Transgenic Seeds of Camelina sativa. PMID:30443260
Long-term investigation of microbial community composition and transcription patterns in a biogas plant undergoing ammonia crisis. PMID:30381904
Homology Inference Based on a Reconciliation Approach for the Comparative Genomics of Protozoa. PMID:30034216
Structural and functional annotation of hypothetical proteins of human adenovirus: prioritizing the novel drug targets. PMID:29212526
Computational design of fully overlapping coding schemes for protein pairs and triplets. PMID:29158504
Helicobacter pylori gene silencing in vivo demonstrates urease is essential for chronic infection. PMID:28644872
Functional and biochemical characterization of a T cell-associated anti-apoptotic protein, GIMAP6. PMID:28381553
Decay of Sexual Trait Genes in an Asexual Parasitoid Wasp. PMID:28172869
Reannotation of Yersinia pestis Strain 91001 Based on Omics Data. PMID:27382076
DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions. PMID:26827237
The organization of domains in proteins obeys Menzerath-Altmann's law of language. PMID:26260760
De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods. PMID:26228684
Application of a hierarchical enzyme classification method reveals the role of gut microbiome in human metabolism. PMID:26099921
Function-selective domain architecture plasticity potentials in eukaryotic genome evolution. PMID:25980317
A conserved P-loop anchor limits the structural dynamics that mediate nucleotide dissociation in EF-Tu. PMID:25566871
The enzymatic nature of an anonymous protein sequence cannot reliably be inferred from superfamily level structural information alone. PMID:25559918
Protein structure annotation resources. PMID:25502191
From discovery to function: the expanding roles of long noncoding RNAs in physiology and disease. PMID:25426780
The SUPERFAMILY 1.75 database in 2014: a doubling of data. PMID:25414345
Comparative genomics of nucleotide metabolism: a tour to the past of the three cellular domains of life. PMID:25230797
Molecular characterization of KU70 and KU80 homologues and exploitation of a KU70-deficient mutant for improving gene deletion frequency in Rhodosporidium toruloides. PMID:25188820
Cross-species gene-family fluctuations reveal the dynamics of horizontal transfers. PMID:24829449
Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms. PMID:24710297
Global patterns of protein domain gain and loss in superkingdoms. PMID:24499935
Comparative analysis of proteomes and functionomes provides insights into origins of cellular diversification. PMID:24492748
A daily-updated tree of (sequenced) life as a reference for genome research. PMID:23778980
Flagellated algae protein evolution suggests the prevalence of lineage-specific rules governing evolutionary rates of eukaryotic proteins. PMID:23563973
A domain-centric solution to functional genomics via dcGO Predictor. PMID:23514627
TnpPred: A Web Service for the Robust Prediction of Prokaryotic Transposases. PMID:23251097
DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. PMID:23161684
Correlating structure and function during the evolution of fibrinogen-related domains. PMID:23076991
Quality assessment of protein model-structures based on structural and functional similarities. PMID:22998498
Subcellular localization of extracytoplasmic proteins in monoderm bacteria: rational secretomics-based strategy for genomic and proteomic analyses. PMID:22912771
Parasites, proteomes and systems: has Descartes' clock run out of time? PMID:22828391
SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone. PMID:22408192
Pleiotropic roles of a ribosomal protein in Dictyostelium discoideum. PMID:22363460
Functional cell surface display and controlled secretion of diverse Agarolytic enzymes by Escherichia coli with a novel ligation-independent cloning vector based on the autotransporter YfaL. PMID:22344647
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
DOMMINO: a database of macromolecular interactions. PMID:22135305
SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss. PMID:22120661
Evolution of vacuolar proton pyrophosphatase domains and volutin granules: clues into the early evolutionary origin of the acidocalcisome. PMID:21974828
Joint scaling laws in functional and evolutionary categories in prokaryotic genomes. PMID:21937509
Genome sequence of the ruminal bacterium Megasphaera elsdenii. PMID:21914887
Computational approaches to selecting and optimising targets for structural biology. PMID:21906678
Are there laws of genome evolution? PMID:21901087
Evolutionary versatility of eukaryotic protein domains revealed by their bigram networks. PMID:21849086
Lafora disease E3-ubiquitin ligase malin is related to TRIM32 at both the phylogenetic and functional level. PMID:21798009
Reductive evolution of proteomes and protein structures. PMID:21730144
Binary classification of protein molecules into intrinsically disordered and ordered segments. PMID:21693062
The proteomic complexity and rise of the primordial ancestor of diversified life. PMID:21612591
Loss of genetic redundancy in reductive genome evolution. PMID:21379323
The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon. PMID:21356104
An infant-associated bacterial commensal utilizes breast milk sialyloligosaccharides. PMID:21288901
The nature of protein domain evolution: shaping the interaction network. PMID:21286315
SUPERFAMILY 1.75 including a domain-centric gene ontology method. PMID:21062816
Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions. PMID:20627862
Save the tree of life or get lost in the woods. PMID:20594329
Recognition of beta-structural motifs using hidden Markov models trained with simulated evolution. PMID:20529918
Genomics and bioinformatics resources for crop improvement. PMID:20208064
Transcriptome analysis of the Cryptocaryon irritans tomont stage identifies potential genes for the detection and control of cryptocaryonosis. PMID:20113487
MicrobesOnline: an integrated portal for comparative and functional genomics. PMID:19906701
Comparative analyses of plant transcription factor databases. PMID:19721806
The CATH hierarchy revisited-structural divergence in domain superfamilies and the continuity of fold space. PMID:19679085
CORAL: aligning conserved core regions across domain families. PMID:19470584
Linking fold, function and phylogeny: a comparative genomics view on protein (domain) evolution. PMID:19440449
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
Augmented training of hidden Markov models to recognize remote homologs via simulated evolution. PMID:19389731
Transient opening of fibronectin type III (FNIII) domains: the interaction of the third FNIII domain of FN with anastellin. PMID:19320499
Protein function annotation by homology-based inference. PMID:19226439
Universal features in the genome-level evolution of protein domains. PMID:19183449
Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation. PMID:19087332
SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny. PMID:19036790
The protein structure initiative structural genomics knowledgebase. PMID:19010965
The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions. PMID:18987007
ExDom: an integrated database for comparative analysis of the exon-intron structures of protein domains in eukaryotes. PMID:18984624
FastBLAST: homology relationships for millions of proteins. PMID:18974889
CentrosomeDB: a human centrosomal proteins database. PMID:18971254
InterPro: the integrative protein signature database. PMID:18940856
The dual transcriptional regulator CysR in Corynebacterium glutamicum ATCC 13032 controls a subset of genes of the McbR regulon in response to the availability of sulphide acceptor molecules. PMID:18854009
A phylogenomic profile of hemerythrins, the nonheme diiron binding respiratory proteins. PMID:18764950
The effectiveness of position- and composition-specific gap costs for protein similarity searches. PMID:18586708
Yeast Pgc1p (YPL206c) controls the amount of phosphatidylglycerol via a phospholipase C-type degradation mechanism. PMID:18434318
BioSAVE: display of scored annotation within a sequence context. PMID:18366701
In silico characterization of proteins: UniProt, InterPro and Integr8. PMID:18219596
Sequence alignment for molecular replacement. PMID:18094464
DBD--taxonomically broad transcription factor predictions: new content and functionality. PMID:18073188
Data growth and its impact on the SCOP database: new developments. PMID:18000004
Multiple domain insertions and losses in the evolution of the Rab prenylation complex. PMID:17705859
Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. PMID:17636889 -
SUPERFAMILY 1.75 including a domain-centric gene ontology method
PubMed citations: 82.
82 articles citing: SUPERFAMILY 1.75 including a domain-centric gene ontology method
What Is Parvalbumin for? PMID:35625584
Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans. PMID:35484634
Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L. PMID:35328546
Genome Analysis of the Broad Host Range Necrotroph Nalanthamala psidii Highlights Genes Associated With Virulence. PMID:35283890
The aqueous humor proteome is intrinsically disordered. PMID:35128080
Erythropoietin Interacts with Specific S100 Proteins. PMID:35053268
Analysis of diverse eukaryotes suggests the existence of an ancestral mitochondrial apparatus derived from the bacterial type II secretion system. PMID:34011950
RUNX1/RUNX1T1 mediates alternative splicing and reorganises the transcriptional landscape in leukemia. PMID:33483506
Signatures of conserved and unique molecular features in Afrotheria. PMID:33441654
Genomic signatures of the evolution of defence against its natural enemies in the poisonous and medicinal plant Datura stramonium (Solanaceae). PMID:33441607
Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing. PMID:32917720
"Mind the Gap": Hi-C Technology Boosts Contiguity of the Globe Artichoke Genome in Low-Recombination Regions. PMID:32817122
Whole genome resequencing of four Italian sweet pepper landraces provides insights on sequence variation in genes of agronomic value. PMID:32514106
Intrinsic Disorder in Tetratricopeptide Repeat Proteins. PMID:32466138
An improved high-quality genome assembly and annotation of Tibetan hulless barley. PMID:32385314
GenDiS database update with improved approach and features to recognize homologous sequences of protein domain superfamilies. PMID:30943284
Genomic Signals of Adaptation towards Mutualism and Sociality in Two Ambrosia Beetle Complexes. PMID:30583535
Strawberry Mottle Virus (Family Secoviridae, Order Picornavirales) Encodes a Novel Glutamic Protease To Process the RNA2 Polyprotein at Two Cleavage Sites. PMID:30541838
The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver. PMID:30445555
Regulatory Genomic Data Cubism. PMID:30428322
Highly Continuous Genome Assembly of Eurasian Perch (Perca fluviatilis) Using Linked-Read Sequencing. PMID:30355765
Evolution of metazoan morphological disparity. PMID:30181261
Do Viruses Exchange Genes across Superkingdoms of Life? PMID:29163404
Genomic assessment in Lactobacillus plantarum links the butyrogenic pathway with glutamine metabolism. PMID:29162929
De novo genome assembly and annotation of Australia's largest freshwater fish, the Murray cod (Maccullochella peelii), from Illumina and Nanopore sequencing read. PMID:28873963
ProtozoaDB 2.0: A Trypanosoma Brucei Case Study. PMID:28726736
Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation. PMID:28717205
InlL from Listeria monocytogenes Is Involved in Biofilm Formation and Adhesion to Mucin. PMID:28473809
Study of intra-inter species protein-protein interactions for potential drug targets identification and subsequent drug design for Escherichia coli O104:H4 C277-11. PMID:28401513
APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins. PMID:28334975
Aberrant coordination geometries discovered in the most abundant metalloproteins. PMID:28142195
SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins - extended Database. PMID:27914894
The plastid genome of some eustigmatophyte algae harbours a bacteria-derived six-gene cluster for biosynthesis of a novel secondary metabolite. PMID:27906133
PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps. PMID:27710935
Machine Learning of Protein Interactions in Fungal Secretory Pathways. PMID:27441920
Evolution of the Calcium-Based Intracellular Signaling System. PMID:27358427
Insight into the Salivary Gland Transcriptome of Lygus lineolaris (Palisot de Beauvois). PMID:26789269
Assessing the Metabolic Diversity of Streptococcus from a Protein Domain Point of View. PMID:26366735
Functional classification of CATH superfamilies: a domain-based approach for protein function annotation. PMID:26139634
INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity. PMID:26019177
Function-selective domain architecture plasticity potentials in eukaryotic genome evolution. PMID:25980317
EvoTol: a protein-sequence based evolutionary intolerance framework for disease-gene prioritization. PMID:25550428
The loose evolutionary relationships between transcription factors and other gene products across prokaryotes. PMID:25515977
The InterPro protein families database: the classification resource after 15 years. PMID:25428371
The SUPERFAMILY 1.75 database in 2014: a doubling of data. PMID:25414345
dcGOR: an R package for analysing ontologies and protein domain annotations. PMID:25356683
Comparative genome analysis of entomopathogenic fungi reveals a complex set of secreted proteins. PMID:25263348
The 'dnet' approach promotes emerging research on cancer patient survival. PMID:25246945
Gene loss rather than gene gain is associated with a host jump from monocots to dicots in the Smut Fungus Melanopsichium pennsylvanicum. PMID:25062916
Bioinformatics on the cloud computing platform Azure. PMID:25050811
Hemoglobins in the genome of the cryptomonad Guillardia theta. PMID:24885221
Classification of intrinsically disordered regions and proteins. PMID:24773235
Genome-wide mapping of cellular protein-RNA interactions enabled by chemical crosslinking. PMID:24747191
Evolution and quantitative comparison of genome-wide protein domain distributions. PMID:24710298
The evolution of human cells in terms of protein innovation. PMID:24692656
Global patterns of protein domain gain and loss in superkingdoms. PMID:24499935
InterProScan 5: genome-scale protein function classification. PMID:24451626
Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models. PMID:24410852
Effective moment feature vectors for protein domain structures. PMID:24391828
Protein domains of unknown function are essential in bacteria. PMID:24381303
SCOP2 prototype: a new approach to protein structure mining. PMID:24293656
CentrosomeDB: a new generation of the centrosomal proteins database for Human and Drosophila melanogaster. PMID:24270791
A daily-updated tree of (sequenced) life as a reference for genome research. PMID:23778980
Transcription factors in Escherichia coli prefer the holo conformation. PMID:23776535
Morphogenesis of Plasmodium zoites is uncoupled from tensile strength. PMID:23773015
CLCAs - a family of metalloproteases of intriguing phylogenetic distribution and with cases of substituted catalytic sites. PMID:23671590
A domain-centric solution to functional genomics via dcGO Predictor. PMID:23514627
How to inherit statistically validated annotation within BAR+ protein clusters. PMID:23514411
Concomitant prediction of function and fold at the domain level with GO-based profiles. PMID:23514233
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. PMID:23203986
D²P²: database of disordered protein predictions. PMID:23203878
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. PMID:23203869
DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. PMID:23161684
Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. PMID:23033316
Protein domain recurrence and order can enhance prediction of protein functions. PMID:22962465
Evolution of oligomeric state through geometric coupling of protein interfaces. PMID:22566652
Cloning, in silico characterization and prediction of three dimensional structure of SbDof1, SbDof19, SbDof23 and SbDof24 proteins from Sorghum [Sorghum bicolor (L.) Moench]. PMID:22476870
Evolutionary inaccuracy of pairwise structural alignments. PMID:22399676
InterPro in 2011: new developments in the family and domain prediction database. PMID:22096229
Translation's coming of age. PMID:21613985
HMMER web server: interactive sequence similarity searching. PMID:21593126
The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. PMID:21177655 -
The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver
PubMed citations: 43.
43 articles citing: The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver
Spatial and temporal proteomics reveals the distinct distributions and dynamics of O-GlcNAcylated proteins. PMID:35705054
Developing a bioinformatics pipeline for comparative protein classification analysis. PMID:35668373
Comparative genomics of the Western Hemisphere soft tick-borne relapsing fever borreliae highlights extensive plasmid diversity. PMID:35641918
Profiles of Natural and Designed Protein-Like Sequences Effectively Bridge Protein Sequence Gaps: Implications in Distant Homology Detection. PMID:35507261
Predicting Protein Conformational Disorder and Disordered Binding Sites. PMID:35507260
Evolutionarily conserved properties of CLCA proteins 1, 3 and 4, as revealed by phylogenetic and biochemical studies in avian homologues. PMID:35417490
Simple, efficient and thorough shotgun proteomic analysis with PatternLab V. PMID:35411045
Hypothetical protein predicted to be tumor suppressor: a protein functional analysis. PMID:35399005
Real-time structure search and structure classification for AlphaFold protein models. PMID:35383281
Activity-Based Protein Profiling for the Identification of Novel Carbohydrate-Active Enzymes Involved in Xylan Degradation in the Hyperthermophilic Euryarchaeon Thermococcus sp. Strain 2319x1E. PMID:35095781
Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology. PMID:34908533
LPI-HyADBS: a hybrid framework for lncRNA-protein interaction prediction integrating feature selection and classification. PMID:34836494
Identification of potential inhibitory analogs of metastasis tumor antigens (MTAs) using bioactive compounds: revealing therapeutic option to prevent malignancy. PMID:34743299
Navigating the amino acid sequence space between functional proteins using a deep learning framework. PMID:34616884
A novel lncRNA-protein interaction prediction method based on deep forest with cascade forest structure. PMID:34556758
Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo. PMID:34428301
The Oldest Co-opted gag Gene of a Human Endogenous Retrovirus Shows Placenta-Specific Expression and Is Upregulated in Diffuse Large B-Cell Lymphomas. PMID:34410386
Nonrefoldability is Pervasive Across the E. coli Proteome. PMID:34308638
An Azo Coupling-Based Chemoproteomic Approach to Systematically Profile the Tyrosine Reactivity in the Human Proteome. PMID:34251175
Diverse Trajectories Drive the Expression of a Giant Virus in the Oomycete Plant Pathogen Phytophthora parasitica. PMID:34140938
Schistosomiasis Drug Discovery in the Era of Automation and Artificial Intelligence. PMID:34135888
The Chaperonin GroESL Facilitates Caulobacter crescentus Cell Division by Supporting the Functions of the Z-Ring Regulators FtsA and FzlA. PMID:33947758
Draft genome of a biparental beetle species, Lethrus apterus. PMID:33902445
Putative LysM Effectors Contribute to Fungal Lifestyle. PMID:33808705
LPI-SKF: Predicting lncRNA-Protein Interactions Using Similarity Kernel Fusions. PMID:33362868
The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies. PMID:33348379
The lncRNA Toolkit: Databases and In Silico Tools for lncRNA Analysis. PMID:33339309
The InterPro protein families and domains database: 20 years on. PMID:33156333
The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities. PMID:33119741
A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community). PMID:32566135
Genome Comparison Identifies Different Bacillus Species in a Bast Fibre-Retting Bacterial Consortium and Provides Insights into Pectin Degrading Genes. PMID:32424209
Probing lncRNA-Protein Interactions: Data Repositories, Models, and Algorithms. PMID:32082358
Whole genome sequencing of Borrelia miyamotoi isolate Izh-4: reference for a complex bacterial genome. PMID:31906865
The protein architecture in Bacteria and Archaea identifies a set of promiscuous and ancient domains. PMID:31856202
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
Bioinformatics analysis of Ras homologue enriched in the striatum, a potential target for Huntington's disease therapy. PMID:31638189
Protein Abundance Biases the Amino Acid Composition of Disordered Regions to Minimize Non-functional Interactions. PMID:31442477
Combined alignments of sequences and domains characterize unknown proteins with remotely related protein search PSISearch2D. PMID:31317184
Bioinformatic and mutational studies of related toxin-antitoxin pairs in Mycobacterium tuberculosis predict and identify key functional residues. PMID:31018964
Rapid identification of novel protein families using similarity searches. PMID:30984369
Compound Heterozygous CHAT Gene Mutations of a Large Deletion and a Missense Variant in a Chinese Patient With Severe Congenital Myasthenic Syndrome With Episodic Apnea. PMID:30914958
Differential proteostatic regulation of insoluble and abundant proteins. PMID:30903148
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classification
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genome
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hidden markov model
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molecular structure
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protein
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structure
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version: FAIRsharing.org: SUPERFAMILY; SUPERFAMILY; DOI: https://doi.org/10.25504/FAIRsharing.frryvx; Last edited: April 26, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
structure databases
metasource: Nucleic Acid Research database catalogue
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protein structure
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
protein folds and structural domains
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:33.505738
ontology and terminology
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version: extracted_at: 2022-11-04T11:33:33.505738
genotype and phenotype
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version: extracted_at: 2022-11-04T11:33:33.505738
metagenomics
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version: extracted_at: 2022-11-04T11:33:33.505738
gene and protein families
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classification
metasource: Fairsharing.orgversion: FAIRsharing.org: SUPERFAMILY; SUPERFAMILY; DOI: https://doi.org/10.25504/FAIRsharing.frryvx; Last edited: April 26, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
genome
metasource: Fairsharing.orgversion: FAIRsharing.org: SUPERFAMILY; SUPERFAMILY; DOI: https://doi.org/10.25504/FAIRsharing.frryvx; Last edited: April 26, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
hidden markov model
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molecular structure
metasource: Fairsharing.orgversion: FAIRsharing.org: SUPERFAMILY; SUPERFAMILY; DOI: https://doi.org/10.25504/FAIRsharing.frryvx; Last edited: April 26, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: SUPERFAMILY; SUPERFAMILY; DOI: https://doi.org/10.25504/FAIRsharing.frryvx; Last edited: April 26, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
structure
metasource: Fairsharing.orgversion: FAIRsharing.org: SUPERFAMILY; SUPERFAMILY; DOI: https://doi.org/10.25504/FAIRsharing.frryvx; Last edited: April 26, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
structure databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
protein structure
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
protein folds and structural domains
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:33:33.505738
ontology and terminology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:33:33.505738
genotype and phenotype
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:33:33.505738
metagenomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:33:33.505738
gene and protein families
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:33:33.505738
classification genome hidden markov model molecular structure protein structure structure protein structure protein folds and structural domains ontology and terminology genotype and phenotype metagenomics gene and protein families
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