FAIRsharing.fyqk5z; Last edited: March 7, 2021, 8:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:04.256341

gene3d
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:04.256341

Other names: gene3d

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

Gene3D uses the information in CATH to predict the locations of structural domains on millions of protein sequences available in public databases. Sequence data from UniProtKB and Ensembl for domains with no experimentally determined structures are scanned against CATH HMMs to predict domain sequence boundaries and make homologous superfamily assignments.

Webpage:

http://gene3d.biochem.ucl.ac.uk

Publications:

Publications
More detailed information about this field from each metasource.

Gene3D: Extensive prediction of globular domains in proteins
PMID: 29112716
metasource: Fairsharing.org
version: FAIRsharing.org: Gene3D; Gene3D; DOI: https://doi.org/10.25504/FAIRsharing.fyqk5z; Last edited: March 7, 2021, 8:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

Functional classification of CATH superfamilies: a domain-based approach for protein function annotation
PMID: 26139634
metasource: Fairsharing.org
version: FAIRsharing.org: Gene3D; Gene3D; DOI: https://doi.org/10.25504/FAIRsharing.fyqk5z; Last edited: March 7, 2021, 8:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

Gene3D: merging structure and function for a Thousand genomes
PMID: 19906693
metasource: Fairsharing.org
version: FAIRsharing.org: Gene3D; Gene3D; DOI: https://doi.org/10.25504/FAIRsharing.fyqk5z; Last edited: March 7, 2021, 8:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences
PMID: 21646335
metasource: Fairsharing.org
version: FAIRsharing.org: Gene3D; Gene3D; DOI: https://doi.org/10.25504/FAIRsharing.fyqk5z; Last edited: March 7, 2021, 8:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:04.256341

http://dx.doi.org/10.1093/nar/gkt1205
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

Gene3D: Extensive prediction of globular domains in proteins PubMed citations: 48.

48 articles citing: Gene3D: Extensive prediction of globular domains in proteins

Contrastive learning on protein embeddings enlightens midnight zone. PMID:35702380
Chromosomal-Level Genome Assembly of the Springtail Tomocerus qinae (Collembola: Tomoceridae). PMID:35298623
Chromosome-Level Genome Assembly of Anthidium xuezhongi Niu & Zhu, 2020 (Hymenoptera: Apoidea: Megachilidae: Anthidiini). PMID:35150256
Protein sequence design with a learned potential. PMID:35136054
A Chromosome-Level Genome Assembly of the Parasitic Wasp Chelonus formosanus Sonan 1932 (Hymenoptera: Braconidae). PMID:35104339
A simple guide to de novo transcriptome assembly and annotation. PMID:35076693
Ultrafast end-to-end protein structure prediction enables high-throughput exploration of uncharacterized proteins. PMID:35074909
Purification, Characterization, and Structural Studies of a Sulfatase from Pedobacter yulinensis. PMID:35011319
Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology. PMID:34908533
Chromosome-Level Genome Assembly of Nephotettix cincticeps (Uhler, 1896) (Hemiptera: Cicadellidae: Deltocephalinae). PMID:34677607
Genome-Wide Identification and Characterization of Polygalacturonase Gene Family in Maize (Zea mays L.). PMID:34639068
Structural bioinformatic analysis of DsbA proteins and their pathogenicity associated substrates. PMID:34504665
Duo: A Signature Based Method to Batch-Analyze Functional Similarities of Proteins. PMID:34475860
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
DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction. PMID:34252926
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
Critical assessment of protein intrinsic disorder prediction. PMID:33875885
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
Biological impact of mutually exclusive exon switching. PMID:33651795
High Quality Aspergillus aculeatus Genomes and Transcriptomes: A Platform for Cellulase Activity Optimization Toward Industrial Applications. PMID:33585410
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
An Educational Bioinformatics Project to Improve Genome Annotation. PMID:33365016
Properties of Cavities in Biological Structures-A Survey of the Protein Data Bank. PMID:33240933
MobiDB: intrinsically disordered proteins in 2021. PMID:33237329
CATH: increased structural coverage of functional space. PMID:33237325
Inhibition of DNA Methylation in Picochlorum soloecismus Alters Algae Productivity. PMID:33193644
Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. PMID:32962098
Chemical structure and genetic organization of the E. coli O6:K15 capsular polysaccharide. PMID:32724125
A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community). PMID:32566135
Minimally altering a critical kinase for low-phytate maize. PMID:32286385
Diversity, structure, and synteny of the cutinase gene of Colletotrichum species. PMID:32076525
FTIP: an accurate and efficient method for global protein surface comparison. PMID:32022843
DisProt: intrinsic protein disorder annotation in 2020. PMID:31713636
Ensembl 2020. PMID:31691826
Identification and Analysis of Long Repeats of Proteins at the Domain Level. PMID:31649924
Genome-Wide Identification of Mango (Mangifera indica L.) Polygalacturonases: Expression Analysis of Family Members and Total Enzyme Activity During Fruit Ripening. PMID:31417586
Combined alignments of sequences and domains characterize unknown proteins with remotely related protein search PSISearch2D. PMID:31317184
Environmental conditions shape the nature of a minimal bacterial genome. PMID:31308405
Innovative strategies for annotating the "relationSNP" between variants and molecular phenotypes. PMID:31114635
A High-quality Draft Genome Assembly of Sinella curviseta: A Soil Model Organism (Collembola). PMID:30668671
SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins. PMID:30445541
CATH: expanding the horizons of structure-based functional annotations for genome sequences. PMID:30398663
InterPro in 2019: improving coverage, classification and access to protein sequence annotations. PMID:30398656
A de Novo EDA-Variant in a Litter of Shorthaired Standard Dachshunds with X-Linked Hypohidrotic Ectodermal Dysplasia. PMID:30397018
cath-resolve-hits: a new tool that resolves domain matches suspiciously quickly. PMID:30295745
Functional classification of CATH superfamilies: a domain-based approach for protein function annotation PubMed citations: 30.

30 articles citing: Functional classification of CATH superfamilies: a domain-based approach for protein function annotation

Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs. PMID:35641150
Exploiting protein family and protein network data to identify novel drug targets for bladder cancer. PMID:35035776
Assigning protein function from domain-function associations using DomFun. PMID:35033002
Role of Position K+4 in the Phosphorylation and Dephosphorylation Reaction Kinetics of the CheY Response Regulator. PMID:34167303
Tracing Evolution Through Protein Structures: Nature Captured in a Few Thousand Folds. PMID:34041266
Structure-based protein function prediction using graph convolutional networks. PMID:34039967
Biological impact of mutually exclusive exon switching. PMID:33651795
Differentially conserved amino acid positions may reflect differences in SARS-CoV-2 and SARS-CoV behaviour. PMID:33560365
CATH: increased structural coverage of functional space. PMID:33237325
GODoc: high-throughput protein function prediction using novel k-nearest-neighbor and voting algorithms. PMID:33203348
Automatic Gene Function Prediction in the 2020's. PMID:33120976
SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals. PMID:33020502
Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences. PMID:31316056
Environmental conditions shape the nature of a minimal bacterial genome. PMID:31308405
A CATH domain functional family based approach to identify putative cancer driver genes and driver mutations. PMID:30670742
CATH: expanding the horizons of structure-based functional annotations for genome sequences. PMID:30398663
Towards region-specific propagation of protein functions. PMID:30304483
Protein CoAlation and antioxidant function of coenzyme A in prokaryotic cells. PMID:29626155
HMMER Cut-off Threshold Tool (HMMERCTTER): Supervised classification of superfamily protein sequences with a reliable cut-off threshold. PMID:29579071
DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier. PMID:29028931
PixelDB: Protein-peptide complexes annotated with structural conservation of the peptide binding mode. PMID:29024246
IntPred: a structure-based predictor of protein-protein interaction sites. PMID:28968673
Structural and Functional View of Polypharmacology. PMID:28860623
An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences. PMID:28777078
CATH: an expanded resource to predict protein function through structure and sequence. PMID:27899584
Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases. PMID:27332861
Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies. PMID:26585402
Gene3D: expanding the utility of domain assignments. PMID:26578585
Diversity in protein domain superfamilies. PMID:26451979
The history of the CATH structural classification of protein domains. PMID:26253692
Gene3D: merging structure and function for a Thousand genomes PubMed citations: 27.

27 articles citing: Gene3D: merging structure and function for a Thousand genomes

A Comparison of Differential Gene Expression in Response to the Onset of Water Stress Between Three Hybrid Brachiaria Genotypes. PMID:33815444
Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne). PMID:31361773
Structural and Functional View of Polypharmacology. PMID:28860623
Using HHsearch to tackle proteins of unknown function: A pilot study with PH domains. PMID:27601190
In silico Identification and Taxonomic Distribution of Plant Class C GH9 Endoglucanases. PMID:27570528
PinSnps: structural and functional analysis of SNPs in the context of protein interaction networks. PMID:27153707
One origin for metallo-β-lactamase activity, or two? An investigation assessing a diverse set of reconstructed ancestral sequences based on a sample of phylogenetic trees. PMID:25185655
Prediction of detailed enzyme functions and identification of specificity determining residues by random forests. PMID:24416252
SeqDepot: streamlined database of biological sequences and precomputed features. PMID:24234005
Alternative splice variants in TIM barrel proteins from human genome correlate with the structural and evolutionary modularity of this versatile protein fold. PMID:23950966
Origin and evolution of protein fold designs inferred from phylogenomic analysis of CATH domain structures in proteomes. PMID:23555236
Evolutionary history of the TBP-domain superfamily. PMID:23376926
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. PMID:23203986
New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures. PMID:23203873
Metagenomic analysis: the challenge of the data bonanza. PMID:22962339
Distribution and prediction of catalytic domains in 2-oxoglutarate dependent dioxygenases. PMID:22862831
GFam: a platform for automatic annotation of gene families. PMID:22790981
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis. PMID:22139938
SitEx: a computer system for analysis of projections of protein functional sites on eukaryotic genes. PMID:22139920
InterPro in 2011: new developments in the family and domain prediction database. PMID:22096229
FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies. PMID:22006843
The InterPro BioMart: federated query and web service access to the InterPro Resource. PMID:21785143
The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences. PMID:21646335
HMMER web server: interactive sequence similarity searching. PMID:21593126
1,000 structures and more from the MCSG. PMID:21219649
Objective sequence-based subfamily classifications of mouse homeodomains reflect their in vitro DNA-binding preferences. PMID:20705649
The CATH database. PMID:20368142
The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences PubMed citations: 5.

5 articles citing: The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences

The language of the protein universe. PMID:26451980
Evolutionary history of the TBP-domain superfamily. PMID:23376926
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. PMID:23203869
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis. PMID:22139938
ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree. PMID:22121228
http://dx.doi.org/10.1093/nar/gkt1205

Tags:

Tags
More detailed information about this field from each metasource.

annotation
metasource: Fairsharing.org
version: FAIRsharing.org: Gene3D; Gene3D; DOI: https://doi.org/10.25504/FAIRsharing.fyqk5z; Last edited: March 7, 2021, 8:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

gene
metasource: Fairsharing.org
version: FAIRsharing.org: Gene3D; Gene3D; DOI: https://doi.org/10.25504/FAIRsharing.fyqk5z; Last edited: March 7, 2021, 8:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

genome
metasource: Fairsharing.org
version: FAIRsharing.org: Gene3D; Gene3D; DOI: https://doi.org/10.25504/FAIRsharing.fyqk5z; Last edited: March 7, 2021, 8:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

hidden markov model
metasource: Fairsharing.org
version: FAIRsharing.org: Gene3D; Gene3D; DOI: https://doi.org/10.25504/FAIRsharing.fyqk5z; Last edited: March 7, 2021, 8:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

protein domain
metasource: Fairsharing.org
version: FAIRsharing.org: Gene3D; Gene3D; DOI: https://doi.org/10.25504/FAIRsharing.fyqk5z; Last edited: March 7, 2021, 8:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

protein interaction
metasource: Fairsharing.org
version: FAIRsharing.org: Gene3D; Gene3D; DOI: https://doi.org/10.25504/FAIRsharing.fyqk5z; Last edited: March 7, 2021, 8:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

protein structure
metasource: Fairsharing.org
version: FAIRsharing.org: Gene3D; Gene3D; DOI: https://doi.org/10.25504/FAIRsharing.fyqk5z; Last edited: March 7, 2021, 8:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

polypeptide_region
metasource: Fairsharing.org
version: FAIRsharing.org: Gene3D; Gene3D; DOI: https://doi.org/10.25504/FAIRsharing.fyqk5z; Last edited: March 7, 2021, 8:42 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

structure databases
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: 2022-11-04T11:27:04.256341

proteins
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:04.256341

protein structure analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:04.256341

sequence analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:04.256341

gene genome hidden markov model protein domain protein interaction protein structure polypeptide region structure protein folds and structural domains proteins protein structure analysis sequence analysis

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SUPERFAMILY

CATH

PASS2

Structural Classification Of Proteins

Integrated resource of protein families, domains and functional sites

VIDA

Genome3D

SCOPe

PCDB

Protein Geometry Database

PTGL

Conserved Domain Database

UniProt Knowledgebase

SISYPHUS

Simple Modular Architecture Research Tool

The Protein Database

ADDA - A Domain Database

Pfam

SAHG

3D interacting domains