Prediction of PK-specific phosphorylation site based on information entropy

Science in China, Series C: Life Sciences

Volumn 51, Issue 1, 2008, Pages 12-20

  Wang, MingHui ^a   Li, ChunHua ^a   Chen, WeiZu ^a   Wang, CunXin ^a  

^a BEIJING UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

Bioinformatics; Information entropy; Phosphorylation prediction

Indexed keywords

PROTEIN KINASE;

AMINO ACID SEQUENCE; ARTICLE; BIOLOGY; CHEMISTRY; CLASSIFICATION; ENTROPY; INTERNET; METABOLISM; MOLECULAR GENETICS; PHOSPHORYLATION; SENSITIVITY AND SPECIFICITY;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; ENTROPY; INTERNET; MOLECULAR SEQUENCE DATA; PHOSPHORYLATION; PROTEIN KINASES; SENSITIVITY AND SPECIFICITY;

EUKARYOTA;

EID: 38049063206     PISSN: 10069305     EISSN: 18622798     Source Type: Journal    
DOI: 10.1007/s11427-008-0012-1     Document Type: Article

References (25)

1. Lou Y, Yao J, Zereshki A, et al. NEK2A interacts with MAD1 and possibly functions as a novel integrator of the spindle checkpoint signaling. J Biol Chem, 2004, 279: 20049-20057
2. Meijer A J, Dubbelhuis P F. Amino acid signalling and the integration of metabolism. Biochem Biophys Res Commun, 2004, 313: 397-403
3. Manning G, Whyte D B, Martinez R, et al. The protein kinase complement of the human genome. Science, 2002, 298: 1912-1934
4. Caenepeel S, Charydczak G, Sudarsanam S, et al. The mouse kinome: Discovery and comparative genomics of all mouse protein kinases. Proc Natl Acad Sci, 2004, 101: 11707-11712
5. Kraft C, Herzog F, Gieffers C, et al. Mitotic regulation of the human anaphase-promoting complex by phosphorylation. EMBO, 2003, 22: 6598-6609
6. Rychlewski L, Kschischo M, Dong L, et al. Target specificity analysis of the Abl kinase using peptide microarray data. J Mol Biol, 2004, 336: 307-311
7. Knight Z A, Schilling B, Row R H, et al. Phosphospecific proteolysis for mapping sites of protein phosphorylation. Nat. Biotechnol., 2003, 21: 1047-1054. Erratum in: Nat. Biotechnol., 2003, 21, 1396
8. Ballif B A, Villen J, Beausoleil S A, et al. Gygi. Phosphoproteomic analysis of the developing mouse brain. Mol Cell Proteomics, 2004, 3: 1093-1101
9. Beausoleil S A, Jedrychowski M, Schwartz D, et al. Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc Natl Acad Sci, 2004, 101: 12130-12135
10. Kreegipuu A, Blom N, Brunak S. PhosphoBase: A database of phosphorylation sites. Release 2.0. Nucleic Acids Res, 1999, 27: 237-239
11. Blom N, Sicheritz-Ponten T, Gupta R, et al. Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics, 2004, 4: 1633-1649
12. Obenauer J C, Cantley L C, Yaffe M B. Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res, 2003, 31: 3635-3641
13. Huang H D, Lee T Y, Tzeng S W, et al. KinasePhos: A web tool for identifying protein kinase-specific phosphorylation sites. Nucleic Acids Res, 2005, 33 (Web Server issue): 226-229
14. Zhou F F, Xue Y, Chen G L, et al. GPS: A novel group-based phosphorylation predicting and scoring method. Biochem Biophys Res Commun, 2004, 325: 1443-1448
15. Xue Y, Li A, Wang L R, et al. PPSP: Prediction of PK-specific phosphorylation site with Bayesian decision theory. BMC Bioinformatics, 2006, 7: 163-173
16. Kim J H, Lee J, Oh B, et al. Prediction of phosphorylation sites using SVMs. Bioinformatics, 2004, 20: 3179-3184
17. Biondi R M, Nebreda A R. Signalling specificity of Ser/Thr protein kinases through docking-site-mediated interactions. Biochem J, 2003, 372(Pt 1): 1-13
18. Holland P M, Cooper J A. Protein modification: Docking sites for kinases. Curr Biol, 1999, 9(9): R329-31
19. Uhlik M T, Temple B, Bencharit S, et al. Structural and evolutionary division of phosphotyrosine binding (PTB) domains. J Mol Biol, 2005, 345(1): 1-20
20. Yaffe M B, Elia A E. Phosphoserine/threonine-binding domains. Curr Opin Cell Biol, 2001, 13(2): 131-138
21. Yaffe M B, Leparc G G, Lai J, et al. A motifbased profile scanning approach for genome-wide prediction of signaling pathways. Nat Biotechnol, 2001, 19(4): 348-353
22. Yaffe M B, Smerdon S J. The use of in vitro peptide-library screens in the analysis of phosphoserine/threonine-binding domain structure and function. Annu Rev Biophys Biomol Struct, 2004, 33: 225-244
23. Diella F, Cameron S, Gemund C, et al. Phospho.ELM: A database of experimentally verified phosphorylation sites in eukaryotic proteins. BMC Bioinformatics, 2004, 5(1): 79-83
24. Chen H, Xue Y, Huang N, Yao X, Sun Z. MeMo: a web tool for prediction of protein methylation modifications. Nucleic Acids Res, 2006, 34 (Web Server issue): W249-253
25. Hutti J E, Jarrell E T, Chang J D, et al. A rapid method for determining protein kinase phosphorylation specificity. Nat Methods, 2004, 1(1): 27-29