Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis

被引：76

作者：

Lees, Jonathan ^{[1
]}

Yeats, Corin ^{[1
]}

Perkins, James ^{[1
]}

Sillitoe, Ian ^{[1
]}

Rentzsch, Robert ^{[1
]}

Dessailly, Benoit H. ^{[1
]}

Orengo, Christine ^{[1
]}

机构：

[1] UCL, Inst Struct & Mol Biol, London WC1E 6BT, England

来源：

NUCLEIC ACIDS RESEARCH | 2012年 / 40卷 / D1期

基金：

英国惠康基金; 美国国家卫生研究院; 英国生物技术与生命科学研究理事会;

关键词：

INTERACTION DATABASE; SUPERFAMILIES; UNIFICATION; CATH; WEB;

D O I：

10.1093/nar/gkr1181

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Gene3D http://www.w3.org/1999/xlink">http://gene3d.biochem.ucl.ac.uk is a comprehensive database of protein domain assignments for sequences from the major sequence databases. Domains are directly mapped from structures in the CATH database or predicted using a library of representative profile HMMs derived from CATH superfamilies. As previously described, Gene3D integrates many other protein family and function databases. These facilitate complex associations of molecular function, structure and evolution. Gene3D now includes a domain functional family (FunFam) level below the homologous superfamily level assignments. Additions have also been made to the interaction data. More significantly, to help with the visualization and interpretation of multi-genome scale data sets, we have developed a new, revamped website. Searching has been simplified with more sophisticated filtering of results, along with new tools based on Cytoscape Web, for visualizing protein-protein interaction networks, differences in domain composition between genomes and the taxonomic distribution of individual superfamilies.

引用

页码：D465 / D471

页数：7

共 36 条

[1]

[Anonymous], NUCL ACIDS RES

[2] The IntAct molecular interaction database in 2010 [J].

Aranda, B. ;

Achuthan, P. ;

Alam-Faruque, Y. ;

Armean, I. ;

Bridge, A. ;

Derow, C. ;

Feuermann, M. ;

Ghanbarian, A. T. ;

Kerrien, S. ;

Khadake, J. ;

Kerssemakers, J. ;

Leroy, C. ;

Menden, M. ;

Michaut, M. ;

Montecchi-Palazzi, L. ;

Neuhauser, S. N. ;

Orchard, S. ;

Perreau, V. ;

Roechert, B. ;

van Eijk, K. ;

Hermjakob, H. .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D525-D531

[3] Gene Ontology: tool for the unification of biology [J].

Ashburner, M ;

Ball, CA ;

Blake, JA ;

Botstein, D ;

Butler, H ;

Cherry, JM ;

Davis, AP ;

Dolinski, K ;

Dwight, SS ;

Eppig, JT ;

Harris, MA ;

Hill, DP ;

Issel-Tarver, L ;

Kasarskis, A ;

Lewis, S ;

Matese, JC ;

Richardson, JE ;

Ringwald, M ;

Rubin, GM ;

Sherlock, G .

NATURE GENETICS, 2000, 25 (01) :25-29

[4]

Bateman A, 2004, NUCLEIC ACIDS RES, V32, pD138, DOI [10.1093/nar/gkp985, 10.1093/nar/gkh121, 10.1093/nar/gkr1065]

[5] The Protein Data Bank [J].

Berman, HM ;

Westbrook, J ;

Feng, Z ;

Gilliland, G ;

Bhat, TN ;

Weissig, H ;

Shindyalov, IN ;

Bourne, PE .

NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :235-242

[6] Comparative analysis and unification of domain-domain interaction networks [J].

Bjorkholm, Patrik ;

Sonnhammer, Erik L. L. .

BIOINFORMATICS, 2009, 25 (22) :3020-3025

[7]

Boutet Emmanuel, 2007, V406, P89

[8] The BioGRID interaction database:: 2008 update [J].

Breitkreutz, Bobby-Joe ;

Stark, Chris ;

Reguly, Teresa ;

Boucher, Lorrie ;

Breitkreutz, Ashton ;

Livstone, Michael ;

Oughtred, Rose ;

Lackner, Daniel H. ;

Bahler, Jurg ;

Wood, Valerie ;

Dolinski, Kara ;

Tyers, Mike .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D637-D640

[9] MINT: the molecular INTeraction database [J].

Chatr-aryamontri, Andrew ;

Ceol, Arnaud ;

Palazzi, Luisa Montecchi ;

Nardelli, Giuliano ;

Schneider, Maria Victoria ;

Castagnoli, Luisa ;

Cesareni, Gianni .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D572-D574

[10] The CATH Hierarchy Revisited-Structural Divergence in Domain Superfamilies and the Continuity of Fold Space [J].

Cuff, Alison ;

Redfern, Oliver C. ;

Greene, Lesley ;

Sillitoe, Ian ;

Lewis, Tony ;

Dibley, Mark ;

Reid, Adam ;

Pearl, Frances ;

Dallman, Tim ;

Todd, Annabel ;

Garratt, Richard ;

Thornton, Janet ;

Orengo, Christine .

STRUCTURE, 2009, 17 (08) :1051-1062

← 1 2 3 4 →