Large-scale mapping of human protein interactome using structural complexes

EMBO Reports

Volumn 13, Issue 3, 2012, Pages 266-271

  Tyagi, Manoj ^a   Hashimoto, Kosuke ^a   Shoemaker, Benjamin A ^a   Wuchty, Stefan ^a   Panchenko, Anna R ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

IBIS; protein complexes; protein interactions; protein structures

Indexed keywords

PROTEIN;

ARTICLE; GENETIC CONSERVATION; HIGH THROUGHPUT SCREENING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN INTERACTION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; HUMANS; MULTIPROTEIN COMPLEXES; PROTEIN BINDING; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN INTERACTION MAPPING; PROTEOMICS; SOFTWARE;

EID: 84857788445     PISSN: 1469221X     EISSN: 14693178     Source Type: Journal    
DOI: 10.1038/embor.2011.261     Document Type: Article

References (22)

1. Venkatesan K et al (2009) An empirical framework for binary interactome mapping. Nat Methods 6: 83-90
2. Aloy P, Russell RB (2002) Interrogating protein interaction networks through structural biology. Proc Natl Acad Sci USA 99: 5896-5901 (Pubitemid 34493236)
3. Kim PM, Lu LJ, Xia Y, Gerstein MB (2006) Relating three-dimensional structures to protein networks provides evolutionary insights. Science 314: 1938-1941 (Pubitemid 46026118)
4. Tuncbag N, Gursoy A, Nussinov R, Keskin O (2011) Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nat Protoc 6: 1341-1354
5. Pruitt KD, Tatusova T, Klimke W, Maglott DR (2009) NCBI reference sequences: current status, policy and new initiatives. Nucleic Acids Res 37: D32-D36
6. Shoemaker BA, Zhang D, Thangudu RR, Tyagi M, Fong JH, Marchler-Bauer A, Bryant SH, Madej T, Panchenko AR (2010) Inferred Biomolecular Interaction Server-a web server to analyze and predict protein interacting partners and binding sites. Nucleic Acids Res 38: D518-D524
7. Shoemaker BA, Zhang D, Tyagi M, Thangudu RR, Fong JH, Marchler-Bauer A, Bryant SH, Madej T, Panchenko AR (2012) IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins. Nucleic Acids Res 40: D834-D840
8. Krissinel E, Henrick K (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372: 774-797 (Pubitemid 47321791)
9. Croft D et al (2011) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 39: D691-D697
10. Ceol A, Chatr Aryamontri A, Licata L, Peluso D, Briganti L, Perfetto L, Castagnoli L, Cesareni G (2010) MINT, the molecular interaction database: 2009 update. Nucleic Acids Res 38: D532-D539
11. Keshava Prasad TS et al (2009) Human Protein Reference Database-2009 update. Nucleic Acids Res 37: D767-D772
12. Subramanian A et al (2005) Gene set enrichment analysis: a knowledgebased approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102: 15545-15550 (Pubitemid 41528093)
13. Consortium GO (2008) The gene ontology project in 2008. Nucleic Acids Res 36: D440-D444
14. Barabasi AL, Oltvai ZN (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5: 101-113 (Pubitemid 38160277)
15. Goto N, Prins P, Nakao M, Bonnal R, Aerts J, Katayama T (2010) BioRuby: bioinformatics software for the Ruby programming language. Bioinformatics 26: 2617-2619
16. Sayers EW et al (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 39: D38-D51
17. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504 (Pubitemid 37428274)
18. Wang Y, Bryant S, Tatusov R, Tatusova T (2000) Links from genome proteins to known 3-D structures. Genome Res 10: 1643-1647
19. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28: 235-242 (Pubitemid 30047768)
20. Gibrat JF, Madej T, Bryant SH (1996) Surprising similarities in structure comparison. Curr Opin Struct Biol 6: 377-385 (Pubitemid 26197439)
21. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32: D277-D280 (Pubitemid 38081656)
22. Goh KI, Oh E, Jeong H, Kahng B, Kim D (2002) Classification of scale-free networks. Proc Natl Acad Sci USA 99: 12583-12588