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Gene3D specifications


Unique identifier OMICS_02891
Name Gene3D
Restrictions to use None
Data access File download, Browse
Version 14.0
Maintained Yes


  • person_outline Jonathan G. Lees

Publications for Gene3D

Gene3D citations


Structural and functional dissection of differentially expressed tomato WRKY transcripts in host defense response against the vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici)

PLoS One
PMCID: 5927432
PMID: 29709017
DOI: 10.1371/journal.pone.0193922

[…] redicted Tomato Interactome Resource (PTIR) database [] using comparative protein interactive network suggested for Arabidopsis WRKY33 interacting partners.CATH/Gene3D AnalysisThe WRKY protein sequences were analyzed for their structural classification using CATH server []. The CATH database provides the hierarchical classification of […]


HMMER Cut off Threshold Tool (HMMERCTTER): Supervised classification of superfamily protein sequences with a reliable cut off threshold

PLoS One
PMCID: 5868777
PMID: 29579071
DOI: 10.1371/journal.pone.0193757

[…] subfamilies were analyzed for function shifts by means of the identification of Specificity Determining Positions (SDPs), resulting in the FunShift database []. GEMMA was used to subcluster the CATH-Gene3D resource resulting in FunFHMMER []. Here an automated cut-off was provided by a functional coherence index, also based on SDPs. CDD [] is a domain database that includes an automated hierarchic […]


The Candida albicans ENO1 gene encodes a transglutaminase involved in growth, cell division, morphogenesis, and osmotic protection

PMCID: 5868267
PMID: 29386353
DOI: 10.1074/jbc.M117.810440

[…] networks with the STRING program ( () were used to determine interactions maps and interactors for enolase. The structural classification of enolase was performed at the CATH/Gene3D (version 4.1) website ( (). A search of domains was performed in the Protein Sequence Analysis and Classification database at the European Bioinformatics Institute (Int […]


Comparative Genomics Highlights Symbiotic Capacities and High Metabolic Flexibility of the Marine Genus Pseudovibrio

Genome Biol Evol
PMCID: 5765558
PMID: 29319806
DOI: 10.1093/gbe/evx271

[…] 5.4-47.0 () was used to classify the genes and to predict domains and sites. At runtime, the following databases were selected: TIGRFAM, ProDom, SMART, PROSITE, PfamA, PRINTS, SUPERFAMILY, Coils, and Gene3d. PRIAM (), SignalP 4.0 (), and TMHMM () were used to assign Enzyme Commission numbers (ECs), to detect signal peptides, and to detect transmembrane protein topology, respectively. Predictions a […]


Identification of the Autochaperone Domain in the Type Va Secretion System (T5aSS): Prevalent Feature of Autotransporters with a β Helical Passenger

Front Microbiol
PMCID: 5767081
PMID: 29375499
DOI: 10.3389/fmicb.2017.02607

[…] Functional motifs were searched using InterProScan v5.22 (Jones et al., ) and interrogating InterPro (IPR) v61.0 database (Finn et al., ), which includes CATH-Gene3D v4.1 (Sillitoe et al., ; Lam et al., ), CDD (Marchler-Bauer et al., ), MobiDB v2.3.2014.07 (Potenza et al., ), HAMAP (Pedruzzi et al., ), PANTHER v11.1 (Mi et al., ), Pfam v30.0 (Finn et al., ) […]


Genomic assessment in Lactobacillus plantarum links the butyrogenic pathway with glutamine metabolism

Sci Rep
PMCID: 5698307
PMID: 29162929
DOI: 10.1038/s41598-017-16186-8

[…] ;) against all the available databases (ProSiteProfiles-20.119), PANTHER-10.0, Coils-2.2.1, PIRSF-3.01, Hamap-201511.02, Pfam-29.0, ProSitePatterns-20.119, SUPERFAMILY-1.75, ProDom-2006.1, SMART-7.1, Gene3D-3.5.0 and TIGRFAM-15.0. Additional information on metabolic pathways was highlighted using the KASS tool, adopting the bidirectional best-hit default mode, against all known enzymes of L. plant […]


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Gene3D institution(s)
Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK; Department of Infectious Disease Epidemiology, Imperial College, London, UK
Gene3D funding source(s)
BBSRC [BB/L002817/1]; Cancer Research UK [A16567]

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