Gene3D: merging structure and function for a Thousand genomes

被引：37

作者：

Lees, Jonathan ^{[1
]}

Yeats, Corin ^{[1
]}

Redfern, Oliver ^{[1
]}

Clegg, Andrew ^{[1
]}

Orengo, Christine ^{[1
]}

机构：

[1] UCL, Dept Biochem & Mol Biol, London WC1 6BT, England

来源：

NUCLEIC ACIDS RESEARCH | 2010年 / 38卷

基金：

美国国家卫生研究院;

关键词：

PROTEIN; RESOURCE; RECOGNITION; PREDICTION; SEQUENCE; DATABASE;

D O I：

10.1093/nar/gkp987

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：

Over the last 2 years the Gene3D resource has been significantly improved, and is now more accurate and with a much richer interactive display via the Gene3D website (http://gene3d.biochem.ucl.ac.uk/). Gene3D provides accurate structural domain family assignments for over 1100 genomes and nearly 10 000 000 proteins. A hidden Markov model library, constructed from the manually curated CATH structural domain hierarchy, is used to search UniProt, RefSeq and Ensembl protein sequences. The resulting matches are refined into simple multi-domain architectures using a recently developed in-house algorithm, DomainFinder 3 (available at: ftp://ftp.biochem.ucl.ac.uk/pub/gene3d_data/DomainFinder3/). The domain assignments are integrated with multiple external protein function descriptions (e. g. Gene Ontology and KEGG), structural annotations (e. g. coiled coils, disordered regions and sequence polymorphisms) and family resources (e. g. Pfam and eggNog) and displayed on the Gene3D website. The website allows users to view descriptions for both single proteins and genes and large protein sets, such as superfamilies or genomes. Subsets can then be selected for detailed investigation or associated functions and interactions can be used to expand explorations to new proteins. Gene3D also provides a set of services, including an interactive genome coverage graph visualizer, DAS annotation resources, sequence search facilities and SOAP services.

引用

页码：D296 / D300

页数：5

共 26 条

[1] 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

[2] The Universal Protein Resource (UniProt) 2009 [J].

Bairoch, Amos ;

Consortium, UniProt ;

Bougueleret, Lydie ;

Altairac, Severine ;

Amendolia, Valeria ;

Auchincloss, Andrea ;

Argoud-Puy, Ghislaine ;

Axelsen, Kristian ;

Baratin, Delphine ;

Blatter, Marie-Claude ;

Boeckmann, Brigitte ;

Bolleman, Jerven ;

Bollondi, Laurent ;

Boutet, Emmanuel ;

Quintaje, Silvia Braconi ;

Breuza, Lionel ;

Bridge, Alan ;

deCastro, Edouard ;

Ciapina, Luciane ;

Coral, Danielle ;

Coudert, Elisabeth ;

Cusin, Isabelle ;

Delbard, Gwennaelle ;

Dornevil, Dolnide ;

Roggli, Paula Duek ;

Duvaud, Severine ;

Estreicher, Anne ;

Famiglietti, Livia ;

Feuermann, Marc ;

Gehant, Sebastian ;

Farriol-Mathis, Nathalie ;

Ferro, Serenella ;

Gasteiger, Elisabeth ;

Gateau, Alain ;

Gerritsen, Vivienne ;

Gos, Arnaud ;

Gruaz-Gumowski, Nadine ;

Hinz, Ursula ;

Hulo, Chantal ;

Hulo, Nicolas ;

James, Janet ;

Jimenez, Silvia ;

Jungo, Florence ;

Junker, Vivien ;

Kappler, Thomas ;

Keller, Guillaume ;

Lachaize, Corinne ;

Lane-Guermonprez, Lydie ;

Langendijk-Genevaux, Petra ;

Lara, Vicente .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D169-D174

[3] The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data [J].

Berman, Helen ;

Henrick, Kim ;

Nakamura, Haruki ;

Markley, John L. .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D301-D303

[4] 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

[5] The CATH classification revisited-architectures reviewed and new ways to characterize structural divergence in superfamilies [J].

Cuff, Alison L. ;

Sillitoe, Ian ;

Lewis, Tony ;

Redfern, Oliver C. ;

Garratt, Richard ;

Thornton, Janet ;

Orengo, Christine A. .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D310-D314

[6] The Pfam protein families database [J].

Finn, Robert D. ;

Tate, John ;

Mistry, Jaina ;

Coggill, Penny C. ;

Sammut, Stephen John ;

Hotz, Hans-Rudolf ;

Ceric, Goran ;

Forslund, Kristoffer ;

Eddy, Sean R. ;

Sonnhammer, Erik L. L. ;

Bateman, Alex .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D281-D288

[7] Ensembl 2009 [J].

Hubbard, T. J. P. ;

Aken, B. L. ;

Ayling, S. ;

Ballester, B. ;

Beal, K. ;

Bragin, E. ;

Brent, S. ;

Chen, Y. ;

Clapham, P. ;

Clarke, L. ;

Coates, G. ;

Fairley, S. ;

Fitzgerald, S. ;

Fernandez-Banet, J. ;

Gordon, L. ;

Graf, S. ;

Haider, S. ;

Hammond, M. ;

Holland, R. ;

Howe, K. ;

Jenkinson, A. ;

Johnson, N. ;

Kahari, A. ;

Keefe, D. ;

Keenan, S. ;

Kinsella, R. ;

Kokocinski, F. ;

Kulesha, E. ;

Lawson, D. ;

Longden, I. ;

Megy, K. ;

Meidl, P. ;

Overduin, B. ;

Parker, A. ;

Pritchard, B. ;

Rios, D. ;

Schuster, M. ;

Slater, G. ;

Smedley, D. ;

Spooner, W. ;

Spudich, G. ;

Trevanion, S. ;

Vilella, A. ;

Vogel, J. ;

White, S. ;

Wilder, S. ;

Zadissa, A. ;

Birney, E. ;

Cunningham, F. ;

Curwen, V. .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D690-D697

[8] InterPro: the integrative protein signature database [J].

Hunter, Sarah ;

Apweiler, Rolf ;

Attwood, Teresa K. ;

Bairoch, Amos ;

Bateman, Alex ;

Binns, David ;

Bork, Peer ;

Das, Ujjwal ;

Daugherty, Louise ;

Duquenne, Lauranne ;

Finn, Robert D. ;

Gough, Julian ;

Haft, Daniel ;

Hulo, Nicolas ;

Kahn, Daniel ;

Kelly, Elizabeth ;

Laugraud, Aurelie ;

Letunic, Ivica ;

Lonsdale, David ;

Lopez, Rodrigo ;

Madera, Martin ;

Maslen, John ;

McAnulla, Craig ;

McDowall, Jennifer ;

Mistry, Jaina ;

Mitchell, Alex ;

Mulder, Nicola ;

Natale, Darren ;

Orengo, Christine ;

Quinn, Antony F. ;

Selengut, Jeremy D. ;

Sigrist, Christian J. A. ;

Thimma, Manjula ;

Thomas, Paul D. ;

Valentin, Franck ;

Wilson, Derek ;

Wu, Cathy H. ;

Yeats, Corin .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D211-D215

[9] eggNOG: automated construction and annotation of orthologous groups of genes [J].

Jensen, Lars Juhl ;

Julien, Philippe ;

Kuhn, Michael ;

von Mering, Christian ;

Muller, Jean ;

Doerks, Tobias ;

Bork, Peer .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D250-D254

[10] KEGG for linking genomes to life and the environment [J].

Kanehisa, Minoru ;

Araki, Michihiro ;

Goto, Susumu ;

Hattori, Masahiro ;

Hirakawa, Mika ;

Itoh, Masumi ;

Katayama, Toshiaki ;

Kawashima, Shuichi ;

Okuda, Shujiro ;

Tokimatsu, Toshiaki ;

Yamanishi, Yoshihiro .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D480-D484

← 1 2 3 →