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

Nucleic Acids Research

Volumn 42, Issue D1, 2014, Pages

  Mosca, Roberto ^a   Céol, Arnaud ^a,b   Stein, Amelie ^c   Olivella, Roger ^a   Aloy, Patrick ^a,d  

^a INSTITUTE FOR RESEARCH IN BIOMEDICINE   (Spain)

^b ISTITUTO ITALIANO DI TECNOLOGIA   (Italy)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; INFORMATION PROCESSING; INFORMATION RETRIEVAL; ONLINE SYSTEM; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; WEB BROWSER; CHEMICAL STRUCTURE; INTERNET; PROTEIN ANALYSIS; PROTEIN DOMAIN; 3D INTERACTING DOMAIN DATA BASE; AUTOMATION; DATA BASE; PROTEIN BINDING; PROTEIN DATA BANK; PROTEIN MOTIF; THREE DIMENSIONAL IMAGING;

DATABASES, PROTEIN; INTERNET; MODELS, MOLECULAR; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN INTERACTION MAPPING; PROTEIN INTERACTION MAPS;

AMINO ACID;

EID: 84891779335     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt887     Document Type: Article

References (36)

1. Yu, H., Braun, P., Yildirim, M.A., Lemmens, I., Venkatesan, K., Sahalie, J., Hirozane-Kishikawa, T., Gebreab, F., Li, N., Simonis, N. et al. (2008) High-quality binary protein interaction map of the yeast interactome network. Science, 322, 104-110.
2. Arabidopsis Interactome Mapping Consortium. (2011) Evidence for network evolution in an Arabidopsis interactome map. Science, 333, 601-607.
3. Rual, J.F., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., Berriz, G.F., Gibbons, F.D., Dreze, M., Ayivi-Guedehoussou, N. et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature, 437, 1173-1178.
4. Rose, P.W., Bi, C., Bluhm, W.F., Christie, C.H., Dimitropoulos, D., Dutta, S., Green, R.K., Goodsell, D.S., Prlic, A., Quesada, M. et al. (2013) The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res., 41, D475-D482.
5. Schuster-Bockler, B. and Bateman, A. (2007) Reuse of structural domain-domain interactions in protein networks. BMC Bioinformatics, 8, 259.
6. Mosca, R., Ceol, A. and Aloy, P. (2013) Interactome3D: adding structural details to protein networks. Nat. Methods, 10, 47-53.
7. Meyer, M.J., Das, J., Wang, X. and Yu, H. (2013) INstruct: a database of high-quality 3D structurally resolved protein interactome networks. Bioinformatics, 29, 1577-1579.
8. Shoemaker, B.A., Panchenko, A.R. and Bryant, S.H. (2006) Finding biologically relevant protein domain interactions: conserved binding mode analysis. Protein Sci., 15, 352-361.
9. Davis, F.P. and Sali, A. (2005) PIBASE: a comprehensive database of structurally defined protein interfaces. Bioinformatics, 21, 1901-1907.
10. Finn, R.D., Marshall, M. and Bateman, A. (2005) iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics, 21, 410-412.
11. Gong, S., Yoon, G., Jang, I., Bolser, D., Dafas, P., Schroeder, M., Choi, H., Cho, Y., Han, K., Lee, S. et al. (2005) PSIbase: a database of Protein Structural Interactome map (PSIMAP). Bioinformatics, 21, 2541-2543.
12. Yellaboina, S., Tasneem, A., Zaykin, D.V., Raghavachari, B. and Jothi, R. (2011) DOMINE: a comprehensive collection of known and predicted domain-domain interactions. Nucleic Acids Res., 39, D730-D735.
13. Jefferson, E.R., Walsh, T.P., Roberts, T.J. and Barton, G.J. (2007) SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. Nucleic Acids Res., 35, D580-D589.
14. Encinar, J.A., Fernandez-Ballester, G., Sanchez, I.E., Hurtado-Gomez, E., Stricher, F., Beltrao, P. and Serrano, L. (2009) ADAN: a database for prediction of protein-protein interaction of modular domains mediated by linear motifs. Bioinformatics, 25, 2418-2424.
15. Pugalenthi, G., Bhaduri, A. and Sowdhamini, R. (2006) iMOTdb-A comprehensive collection of spatially interacting motifs in proteins. Nucleic Acids Res., 34, D285-D286.
16. Vanhee, P., Reumers, J., Stricher, F., Baeten, L., Serrano, L., Schymkowitz, J. and Rousseau, F. (2010) PepX: a structural database of non-redundant protein-peptide complexes. Nucleic Acids Res., 38, D545-D551.
17. Das, A.A., Sharma, O.P., Kumar, M.S., Krishna, R. and Mathur, P.P. (2013) PepBind: a comprehensive database and computational tool for analysis of protein-peptide interactions. Genomics Proteomics Bioinformatics, 11, 241-246.
18. Murzin, A.G., Brenner, S.E., Hubbard, T. and Chothia, C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
19. Sillitoe, I., Cuff, A.L., Dessailly, B.H., Dawson, N.L., Furnham, N., Lee, D., Lees, J.G., Lewis, T.E., Studer, R.A., Rentzsch, R. et al. (2013) New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures. Nucleic Acids Res., 41, D490-D498.
20. Punta, M., Coggill, P.C., Eberhardt, R.Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J. et al. (2012) The Pfam protein families database. Nucleic Acids Res., 40, D290-D301.
21. Stein, A., Russell, R.B. and Aloy, P. (2005) 3did: interacting protein domains of known three-dimensional structure. Nucleic Acids Res., 33, D413-D417.
22. Stein, A., Panjkovich, A. and Aloy, P. (2009) 3did Update: domaindomain and peptide-mediated interactions of known 3D structure. Nucleic Acids Res., 37, D300-D304.
23. Stein, A., Ceol, A. and Aloy, P. (2011) 3did: identification and classification of domain-based interactions of known three-dimensional structure. Nucleic Acids Res., 39, D718-D723.
24. Chakrabarti, P. and Janin, J. (2002) Dissecting protein-protein recognition sites. Proteins, 47, 334-343.
25. Finn, R.D., Clements, J. and Eddy, S.R. (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res., 39, W29-W37.
26. Aloy, P. and Russell, R.B. (2002) Interrogating protein interaction networks through structural biology. Proc. Natl Acad. Sci. USA, 99, 5896-5901.
27. Aloy, P. and Russell, R.B. (2003) InterPreTS: protein interaction prediction through tertiary structure. Bioinformatics, 19, 161-162.
28. Scott, J.D. and Pawson, T. (2009) Cell signaling in space and time: where proteins come together and when they're apart. Science, 326, 1220-1224.
29. Ejiri, K., Taniguchi, H., Ishihara, K., Hara, Y. and Baba, S. (1990) Possible involvement of cholinergic nicotinic receptor in insulin release from isolated rat islets. Diabetes Res. Clin. Pract., 8, 193-199.
30. Dinkel, H., Michael, S., Weatheritt, R.J., Davey, N.E., Van Roey, K., Altenberg, B., Toedt, G., Uyar, B., Seiler, M., Budd, A. et al. (2012) ELM-the database of eukaryotic linear motifs. Nucleic Acids Res., 40, D242-D251.
31. Edwards, R.J., Davey, N.E., O'Brien, K. and Shields, D.C. (2012) Interactome-wide prediction of short, disordered protein interaction motifs in humans. Mol. Biosyst., 8, 282-295.
32. Hugo, W., Song, F., Aung, Z., Ng, S.K. and Sung, W.K. (2010) SLiM on Diet: finding short linear motifs on domain interaction interfaces in Protein Data Bank. Bioinformatics, 26, 1036-1042.
33. Stein, A. and Aloy, P. (2010) Novel peptide-mediated interactions derived from high-resolution 3-dimensional structures. PLoS Computat. Biol., 6, e1000789.
34. The Gene Ontology Consortium. (2013) Gene Ontology annotations and resources. Nucleic Acids Res., 41, D530-D535.
35. Lopes, C.T., Franz, M., Kazi, F., Donaldson, S.L., Morris, Q. and Bader, G.D. (2010) Cytoscape Web: an interactive web-based network browser. Bioinformatics, 26, 2347-2348.
36. Mosca, R., Pons, T., Ceol, A., Valencia, A. and Aloy, P. (2013) Towards a detailed atlas of protein-protein interactions. Curr. Opin. Struct. Biol., 23, 929-940.