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Gene3D specifications

Information


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

Maintainer


  • person_outline Jonathan G. Lees

Publications for Gene3D

Gene3D citations

 (103)
library_books

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

2018
PLoS One
PMCID: 5927432
PMID: 29709017
DOI: 10.1371/journal.pone.0193922

[…] redicted Tomato Interactome Resource (PTIR) database http://bdg.hfut.edu.cn/ptir/index.html [] 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 http://www.cathdb.info/ []. The CATH database provides the hierarchical classification of […]

library_books

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

2018
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 […]

library_books

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

2018
PMCID: 5868267
PMID: 29386353
DOI: 10.1074/jbc.M117.810440

[…] networks with the STRING program (https://string-db.org/)5 () 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 (http://www.cathdb.info/)5 (). A search of domains was performed in the Protein Sequence Analysis and Classification database at the European Bioinformatics Institute (Int […]

library_books

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

2018
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 […]

library_books

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

2018
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., ) […]

library_books

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

2017
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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