3did: a catalog of domain-based interactions of known three-dimensional structure

被引：201

作者：

Mosca, Roberto ^{[1
]}

Ceol, Arnaud ^{[1
,2
]}

Stein, Amelie ^{[3
,4
]}

Olivella, Roger ^{[1
]}

Aloy, Patrick ^{[1
,5
]}

机构：

[1] Inst Res Biomed IRB Barcelona, Joint IRB BSC Program Computat Biol, Barcelona 08028, Spain

[2] Ist Italiano Tecnol, Ctr Genom Sci IIT SEMM, I-20139 Milan, Italy

[3] Univ Calif San Francisco, Calif Inst Quantitat Biomed Res Qb3, San Francisco, CA 94158 USA

[4] Univ Calif San Francisco, Dept Bioengn & Therapeut Sci, San Francisco, CA 94158 USA

[5] Inst Catalana Recerca & Estudis Avancats, Barcelona 08010, Spain

来源：

NUCLEIC ACIDS RESEARCH | 2014年 / 42卷 / D1期

关键词：

PROTEIN-PROTEIN INTERACTION; COMPREHENSIVE DATABASE; MAP; CLASSIFICATION; PREDICTION; MOTIFS; WEB;

D O I：

10.1093/nar/gkt887

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：

The database of 3D interacting domains (3did, available online for browsing and bulk download at http://3did.irbbarcelona.org) is a catalog of protein-protein interactions for which a high-resolution 3D structure is known. 3did collects and classifies all structural templates of domain-domain interactions in the Protein Data Bank, providing molecular details for such interactions. The current version also includes a pipeline for the discovery and annotation of novel domain-motif interactions. For every interaction, 3did identifies and groups different binding modes by clustering similar interfaces into 'interaction topologies'. By maintaining a constantly updated collection of domain-based structural interaction templates, 3did is a reference source of information for the structural characterization of protein interaction networks. 3did is updated every 6 months.

引用

页码：D374 / D379

页数：6

共 36 条

[1] InterPreTS: protein Interaction Prediction through Tertiary Structure [J].

Aloy, P ;

Russell, RB .

BIOINFORMATICS, 2003, 19 (01) :161-162

[2] Interrogating protein interaction networks through structural biology [J].

Aloy, P ;

Russell, RB .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 (09) :5896-5901

[3]

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

[4] Gene Ontology Annotations and Resources [J].

Blake, J. A. ;

Dolan, M. ;

Drabkin, H. ;

Hill, D. P. ;

Ni, Li ;

Sitnikov, D. ;

Bridges, S. ;

Burgess, S. ;

Buza, T. ;

McCarthy, F. ;

Peddinti, D. ;

Pillai, L. ;

Carbon, S. ;

Dietze, H. ;

Ireland, A. ;

Lewis, S. E. ;

Mungall, C. J. ;

Gaudet, P. ;

Chisholm, R. L. ;

Fey, P. ;

Kibbe, W. A. ;

Basu, S. ;

Siegele, D. A. ;

McIntosh, B. K. ;

Renfro, D. P. ;

Zweifel, A. E. ;

Hu, J. C. ;

Brown, N. H. ;

Tweedie, S. ;

Alam-Faruque, Y. ;

Apweiler, R. ;

Auchinchloss, A. ;

Axelsen, K. ;

Bely, B. ;

Blatter, M-C. ;

Bonilla, C. ;

Bougueleret, L. ;

Boutet, E. ;

Breuza, L. ;

Bridge, A. ;

Chan, W. M. ;

Chavali, G. ;

Coudert, E. ;

Dimmer, E. ;

Estreicher, A. ;

Famiglietti, L. ;

Feuermann, M. ;

Gos, A. ;

Gruaz-Gumowski, N. ;

Hieta, R. .

NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D530-D535

[5] Evidence for Network Evolution in an Arabidopsis Interactome Map [J].

Braun, Pascal ;

Carvunis, Anne-Ruxandra ;

Charloteaux, Benoit ;

Dreze, Matija ;

Ecker, Joseph R. ;

Hill, David E. ;

Roth, Frederick P. ;

Vidal, Marc ;

Galli, Mary ;

Balumuri, Padmavathi ;

Bautista, Vanessa ;

Chesnut, Jonathan D. ;

Kim, Rosa Cheuk ;

de los Reyes, Chris ;

Gilles, Patrick, II ;

Kim, Christopher J. ;

Matrubutham, Uday ;

Mirchandani, Jyotika ;

Olivares, Eric ;

Patnaik, Suswapna ;

Quan, Rosa ;

Ramaswamy, Gopalakrishna ;

Shinn, Paul ;

Swamilingiah, Geetha M. ;

Wu, Stacy ;

Ecker, Joseph R. ;

Dreze, Matija ;

Byrdsong, Danielle ;

Dricot, Amelie ;

Duarte, Melissa ;

Gebreab, Fana ;

Gutierrez, Bryan J. ;

MacWilliams, Andrew ;

Monachello, Dario ;

Mukhtar, M. Shahid ;

Poulin, Matthew M. ;

Reichert, Patrick ;

Romero, Viviana ;

Tam, Stanley ;

Waaijers, Selma ;

Weiner, Evan M. ;

Vidal, Marc ;

Hill, David E. ;

Braun, Pascal ;

Galli, Mary ;

Carvunis, Anne-Ruxandra ;

Cusick, Michael E. ;

Dreze, Matija ;

Romero, Viviana ;

Roth, Frederick P. .

SCIENCE, 2011, 333 (6042) :601-607

[6] Dissecting protein-protein recognition sites [J].

Chakrabarti, P ;

Janin, J .

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2002, 47 (03) :334-343

[7]

Das Arindam Atanu, 2013, Genomics Proteomics & Bioinformatics, V11, P241, DOI 10.1016/j.gpb.2013.03.002

[8] PIBASE: a comprehensive database of structurally defined protein interfaces [J].

Davis, FP ;

Sali, A .

BIOINFORMATICS, 2005, 21 (09) :1901-1907

[9] ELM-the database of eukaryotic linear motifs [J].

Dinkel, Holger ;

Michael, Sushama ;

Weatheritt, Robert J. ;

Davey, Norman E. ;

Van Roey, Kim ;

Altenberg, Brigitte ;

Toedt, Grischa ;

Uyar, Bora ;

Seiler, Markus ;

Budd, Aidan ;

Joedicke, Lisa ;

Dammert, Marcel A. ;

Schroeter, Christian ;

Hammer, Maria ;

Schmidt, Tobias ;

Jehl, Peter ;

McGuigan, Caroline ;

Dymecka, Magdalena ;

Chica, Claudia ;

Luck, Katja ;

Via, Allegra ;

Chatr-Aryamontri, Andrew ;

Haslam, Niall ;

Grebnev, Gleb ;

Edwards, Richard J. ;

Steinmetz, Michel O. ;

Meiselbach, Heike ;

Diella, Francesca ;

Gibson, Toby J. .

NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D242-D251

[10] Interactome-wide prediction of short, disordered protein interaction motifs in humans [J].

Edwards, Richard J. ;

Davey, Norman E. ;

O'Brien, Kevin ;

Shields, Denis C. .

MOLECULAR BIOSYSTEMS, 2012, 8 (01) :282-295

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