Modular composition predicts kinase/substrate interactions

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Liu, Yichuan ^a   Tozeren, Aydin ^a  

^a DREXEL UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANNOTATION TOOL; CELLULAR PROTEINS; COMPLEX DISEASE; DOMAIN COMPOSITION; MODULAR COMPOSITION; PROTEIN PHOSPHORYLATION; SIGNALING PATHWAYS; SUBSTRATE BINDING;

BINDING ENERGY; COMPLEX NETWORKS; DRUG THERAPY; ENZYMES; PHOSPHORYLATION; PROTEINS; TOOLS;

SUBSTRATES;

PHOSPHOTRANSFERASE; PROTEOME;

ARTICLE; ENZYME SPECIFICITY; HUMAN; METABOLISM; PHOSPHORYLATION; PROTEIN BINDING; PROTEIN TERTIARY STRUCTURE; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION;

HUMANS; PHOSPHORYLATION; PHOSPHOTRANSFERASES; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; PROTEOME; SEQUENCE ANALYSIS, PROTEIN; SIGNAL TRANSDUCTION; SUBSTRATE SPECIFICITY;

EID: 77955354765     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-349     Document Type: Article

References (33)

1. Bhattacharyya RP, Remenyi A, Yeh BJ, Lim WA. Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits. Annu Rev Biochem 2006, 75:655-680. 10.1146/annurev.biochem.75.103004.142710, 16756506.
2. Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S. The protein kinase complement of the human genome. Science 2002, 298(5600):1912-1934. 10.1126/science.1075762, 12471243.
3. Kostich M, English J, Madison V, Gheyas F, Wang L, Qiu P, Greene J, Laz TM. Human members of the eukaryotic protein kinase family. Genome Biol 2002, 3(9). RESEARCH0043, 10.1186/gb-2002-3-9-research0043, 126868, 12225582.
4. Rochette-Egly C, Germain P. Dynamic and combinatorial control of gene expression by nuclear retinoic acid receptors (RARs). Nucl Recept Signal 2009, 7:e005. 2686084, 19471584.
5. Remenyi A, Good MC, Lim WA. Docking interactions in protein kinase and phosphatase networks. Curr Opin Struct Biol 2006, 16(6):676-685. 10.1016/j.sbi.2006.10.008, 17079133.
6. Zhou T, Sun L, Humphreys J, Goldsmith EJ. Docking interactions induce exposure of activation loop in the MAP kinase ERK2. Structure 2006, 14(6):1011-1019. 10.1016/j.str.2006.04.006, 16765894.
7. de Castro E, Sigrist CJ, Gattiker A, Bulliard V, Langendijk-Genevaux PS, Gasteiger E, Bairoch A, Hulo N. ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res 2006, (34 Web Server):W362-365. 10.1093/nar/gkl124, 1538847, 16845026.
8. Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, et al. The Pfam protein families database. Nucleic Acids Res 2008, (36 Database):D281-288. 2238907, 18039703.
9. Attwood TK, Croning MD, Flower DR, Lewis AP, Mabey JE, Scordis P, Selley JN, Wright W. PRINTS-S: the database formerly known as PRINTS. Nucleic Acids Res 2000, 28(1):225-227. 10.1093/nar/28.1.225, 102408, 10592232.
10. Corpet F, Servant F, Gouzy J, Kahn D. ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons. Nucleic Acids Res 2000, 28(1):267-269. 10.1093/nar/28.1.267, 102458, 10592243.
11. Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, et al. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res 2001, 29(1):37-40. 10.1093/nar/29.1.37, 29841, 11125043.
12. Diella F, Cameron S, Gemund C, Linding R, Via A, Kuster B, Sicheritz-Ponten T, Blom N, Gibson TJ. Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. BMC Bioinformatics 2004, 5:79. 10.1186/1471-2105-5-79, 449700, 15212693.
13. Evans P, Dampier W, Ungar L, Tozeren A. Prediction of HIV-1 virus-host protein interactions using virus and host sequence motifs. BMC Med Genomics 2009, 2:27. 10.1186/1755-8794-2-27, 2694829, 19450270.
14. Dampier W, Evans P, Ungar L, Tozeren A. Host sequence motifs shared by HIV predict response to antiretroviral therapy. BMC Med Genomics 2009, 2:47. 10.1186/1755-8794-2-47, 2723131, 19627600.
15. Bardwell AJ, Frankson E, Bardwell L. Selectivity of docking sites in MAPK kinases. J Biol Chem 2009, 284(19):13165-13173. 10.1074/jbc.M900080200, 2676048, 19196711.
16. Neduva V, Russell RB. Linear motifs: evolutionary interaction switches. FEBS Lett 2005, 579(15):3342-3345. 10.1016/j.febslet.2005.04.005, 15943979.
17. Skrabanek L, Saini HK, Bader GD, Enright AJ. Computational prediction of protein-protein interactions. Mol Biotechnol 2008, 38(1):1-17. 10.1007/s12033-007-0069-2, 18095187.
18. Shen J, Zhang J, Luo X, Zhu W, Yu K, Chen K, Li Y, Jiang H. Predicting protein-protein interactions based only on sequences information. Proc Natl Acad Sci USA 2007, 104(11):4337-4341. 10.1073/pnas.0607879104, 1838603, 17360525.
19. Bock JR, Gough DA. Predicting protein--protein interactions from primary structure. Bioinformatics 2001, 17(5):455-460. 10.1093/bioinformatics/17.5.455, 11331240.
20. Sprinzak E, Margalit H. Correlated sequence-signatures as markers of protein-protein interaction. J Mol Biol 2001, 311(4):681-692. 10.1006/jmbi.2001.4920, 11518523.
21. Liu M, Chen XW, Jothi R. Knowledge-guided inference of domain-domain interactions from incomplete protein-protein interaction networks. Bioinformatics 2009, 25(19):2492-2499. 10.1093/bioinformatics/btp480, 2752622, 19667081.
22. Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, et al. Human Protein Reference Database--2009 update. Nucleic Acids Res 2009, (37 Database):D767-772. 10.1093/nar/gkn892, 2686490, 18988627.
23. Breitkreutz BJ, Stark C, Reguly T, Boucher L, Breitkreutz A, Livstone M, Oughtred R, Lackner DH, Bahler J, Wood V, et al. The BioGRID Interaction Database: 2008 update. Nucleic Acids Res 2008, (36 Database):D637-640. 2238873, 18000002.
24. Prasad TS, Kandasamy K, Pandey A. Human protein reference database and human proteinpedia as discovery tools for systems biology. Methods Mol Biol 2009, 577:67-79. full_text, 19718509.
25. Mishra GR, Suresh M, Kumaran K, Kannabiran N, Suresh S, Bala P, Shivakumar K, Anuradha N, Reddy R, Raghavan TM, et al. Human protein reference database--2006 update. Nucleic Acids Res 2006, (34 Database):D411-414. 10.1093/nar/gkj141, 1347503, 16381900.
26. Hulo N, Bairoch A, Bulliard V, Cerutti L, Cuche BA, de Castro E, Lachaize C, Langendijk-Genevaux PS, Sigrist CJ. The 20 years of PROSITE. Nucleic Acids Res 2008, (36 Database):D245-249. 2238851, 18003654.
27. Gormley M, Dampier W, Ertel A, Karacali B, Tozeren A. Prediction potential of candidate biomarker sets identified and validated on gene expression data from multiple datasets. BMC Bioinformatics 2007, 8:415. 10.1186/1471-2105-8-415, 2211325, 17963508.
28. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, et al. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 2004, (32 Database):D258-261. 308770, 14681407.
29. Kanehisa M. The KEGG database. Novartis Found Symp 2002, 247:91-101. discussion 101-103, 119-128,244-152, full_text, 12539951.
30. Fu W, Sanders-Beer BE, Katz KS, Maglott DR, Pruitt KD, Ptak RG. Human immunodeficiency virus type 1, human protein interaction database at NCBI. Nucleic Acids Res 2009, (37 Database):D417-422. 10.1093/nar/gkn708, 2686594, 18927109.
31. Superti SV, Martins Dde S, Caierao J, Soares Fda S, Prochnow T, Zavascki AP. Indications of carbapenem resistance evolution through heteroresistance as an intermediate stage in Acinetobacter baumannii after carbapenem administration. Rev Inst Med Trop Sao Paulo 2009, 51(2):111-113.
32. Slaughter BD, Schwartz JW, Li R. Mapping dynamic protein interactions in MAP kinase signaling using live-cell fluorescence fluctuation spectroscopy and imaging. Proc Natl Acad Sci USA 2007, 104(51):20320-20325. 10.1073/pnas.0710336105, 2154429, 18077328.
33. Bhatnagar A, Ghauri AJ, Hope-Ross M, Lip PL. Diabetic retinopathy in pregnancy. Curr Diabetes Rev 2009, 5(3):151-156. 10.2174/157339909788920929, 19689249.