PPSP: Prediction of PK-specific phosphorylation site with Bayesian decision theory

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Xue, Yu ^a   Li, Ao ^a   Wang, Lirong ^a   Feng, Huanqing ^a   Yao, Xuebiao ^a,b  

^a UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^b MOREHOUSE SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BAYESIAN DECISION THEORY; BIOLOGICAL PROCESS; INTRINSIC FEATURES; MOLECULAR MECHANISM; PHOSPHORYLATION SITES; POST-TRANSLATIONAL MODIFICATIONS; SUBSTRATES SPECIFICITIES; UBIQUITOUS APPROACH;

DECISION THEORY; FORECASTING; PROTEINS; TOOLS;

PHOSPHORYLATION;

PROTEIN KINASE; PROTEIN BINDING;

ACCURACY; ARTICLE; BAYES THEOREM; COMPARATIVE STUDY; COMPUTER PROGRAM; CONTROLLED STUDY; DECISION THEORY; ENZYME PHOSPHORYLATION; ENZYME SUBSTRATE; PREDICTION; UBIQUITINATION; AMINO ACID SEQUENCE; BINDING SITE; CHEMISTRY; CLASSIFICATION; MOLECULAR GENETICS; PHOSPHORYLATION; PROCEDURES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; BAYES THEOREM; BINDING SITES; MOLECULAR SEQUENCE DATA; PHOSPHORYLATION; PROTEIN BINDING; PROTEIN KINASES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 33645758540     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-163     Document Type: Article

References (37)

1. Schafmeier T, Haase A, Kaldi K, Scholz J, Fuchs M, Brunner M: Transcriptional feedback of neurospora circadian clock gene by phosphorylation-dependent inactivation of its transcription factor. Cell 2005, 122(2):235-246.
2. Singh CR, Curtis C, Yamamoto Y, Hall NS, Kruse DS, He H, Hannig EM, Asano K: Eukaryotic translation initiation factor 5 is critical for integrity of the scanning preinitiation complex and accurate control of GCN4 translation. Mol Cell Biol 2005, 25(13):5480-5491.
3. Lou Y, Yao J, Zereshki A, Dou Z, Ahmed K, Wang H, Hu J, Wang Y, Yao X: NEK2A interacts with MADI and possibly functions as a novel integrator of the spindle checkpoint signaling. J Biol Chem 2004, 279(19):20049-20057.
4. Liu HY, MacDonald JI, Hryciw T, Li C, Meakin SO: Human tumorous imaginal disc I (TIDI) associates with Trk receptor tyrosine kinases and regulates neurite, outgrowth in nnr5-TrkA cells. J Biol Chem 2005, 280(20):19461-19471.
5. Robinson KN, Manto K, Buchsbaum RJ, MacDonald JI, Mealdn SO: Neurotrophin-dependent tyrosine phosphorylation of Ras guanine-releasing factor I and associated neurite outgrowth is dependent on the HIKE domain of TrkA. J Biol Chem 2005, 280(1):225-235.
6. Pawson T: Specificity in signal transduction: from phosphotyrosine-SH2 domain interactions to complex cellular systems. Cell 2004, 116(2):191-203.
7. Ma L, Chen Z, Erdjument-Bromage H, Tempst P, Pandolfi PP: Phosphorylation and functional inactivation of TSC2 by Erk implications for tuberous sclerosis and cancer pathogenesis. Cell 2005, 121(2):179-193.
8. Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villen J, Li J, Cohn MA, Cantley LC, Gygi SP: Large-scale characterization of HeLa, cell nuclear phosphoproteins. Proc Natl Acad Sci U S A 2004, 101(33):12130-12135.
9. Kreegipuu A, Blom N, Brunak S: PhosphoBase, a database of phosphorylation sites: release 2.0. Nucleic Acids Res 1999, 27(1):237-239.
10. Manning BD, Cantley LC: Hitting the target: emerging technologies in the search for kinase, substrates. Sci STKE 2002, 2002(162):PE49.
11. Kim JH, Lee J, Oh B, Kimm K, Koh I: Prediction of phosphorylation sites using SVMs. Bioinformatics 2004, 20(17):3179-3184.
12. Biondi RM, Nebreda AR: Signalling specificity of Ser/Thr protein kinases through docking-site-mediated interactions. Biochem J 2003, 372(Pt 1): 1-13.
13. Obenauer JC, Cantley LC, Yaffe MB: Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res 2003, 31(13):3635-3641.
14. Uhlik MT, Temple B, Bencharit S, Kimple AJ, Siderovski DP, Johnson GL: Structural and evolutionary division of phosphotyrosine binding (PTB) domains. J Mol Biol 2005, 345(1):1-20.
15. Yaffe MB, Elia AE: Phosphoserine/threonine-binding domains. Curr Opin Cell Biol 2001, 13(2):131-138.
16. Yaffe MB, Leparc GG, Lai J, Obata T, Volinia S, Cantley LC: A motif-based profile scanning approach for genome-wide prediction of signaling pathways. Nat Biotechnol 2001, 19(4):348-353.
17. Yaffe MB, Smerdon SJ: 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.
18. Holland PM, Cooper JA: Protein modification: docking sites for kinases. Curr Biol 1999, 9(9):R329-31.
19. Joughin BA, Tidor B, Yaffe MB: A computational method for the analysis and prediction of protein:phosphopeptide-binding sites. Protein Sci 2005, 14(1):131-139.
20. Ficarro SB, McCleland ML, Stukenberg PT, Burke DJ, Ross MM, Shabanowitz J, Hunt DF, White FM: Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat Biotechnol 2002, 20(3):301-305.
21. Ballif BA, Villen J, Beausoleil SA, Schwartz D, Gygi SP: Phosphoproteomic analysis of the developing mouse brain. Mol Cell Proteomics 2004, 3(11):1093-1101.
22. Blom N, Gammeltoft S, Brunak S: Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J Mol Biol 1999, 294(5):1351-1362.
23. Blom N, Sicheritz-Ponten T, Gupta P, Gammeltoft S, Brunak S: Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics 2004, 4(6):1633-1649.
24. Huang HD, Lee TY, Tzeng SW, Horng JT: KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites. Nucleic Acids Res 2005, 33(Web Server issue):W226-9.
25. Huang HD, Lee TY, Tzeng SW, Wu LC, Horng JT, Tsou AP, Huang KT: Incorporating hidden Markov models for identifying protein kinase-specific phosphorylation sites. J Comput Chem 2005, 26(10):1032-1041.
26. Xue Y, Zhou F, Zhu M, Ahmed K, Chen G, Yao X GPS: a comprehensive www server for phosphorylation sites prediction. Nucleic Acids Res 2005, 33(Web Server issue):W184-7.
27. Zhou FF, Xue Y, Chen GL, Yao X: GPS: a novel group-based phosphorylation predicting and scoring method. Biochem Biophys Res Commun 2004, 325(4):1443-1448.
28. 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(1):79.
29. Duda RO, Hart PE, Stork DG: Pattern classification. 2nd edition. Beijing, China Machine Press; 2004:680.
30. Henikoff S, Henikoff JG: Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A 1992, 89(22):10915-10919.
31. Modrof J, Lymperopoulos K, Roy P: Phosphorylation of bluetongue virus nonstructural protein 2 is essential for formation of viral inclusion bodies. J Virol 2005, 79(15):10023-10031.
32. Horscroft NJ, Roy P: NTP binding and phosphohydrolase activity associated with purified bluetongue virus non-structural protein NS2. J Gen Virol 2000, 81 (Pt 8):1961-1965.
33. Lymperopoulos K, Wirblich C, Brierley I, Roy P: Sequence specificity in the interaction of Bluetongue virus non-structural protein 2 (NS2) with viral RNA. J Biol Chem 2003, 278(34):31722-31730.
34. Taraporewala ZF, Chen D, Patton JT: Multimers of the bluetongue virus nonstructural protein, NS2, possess nucleotidyl phosphatase activity: similarities between NS2 and rotavirus NSP2. Virology 2001,280(2):221-231.
35. Bonet C, Fernandez I, Aran X, Bernues J, Giralt E, Azorin F: The GAGA Protein of Drosophila is Phosphorylated by CK2. J Mol Biol 2005, 351(3):562-572.
36. Arrigoni G, Marin O, Pagano MA, Settimo L, Paolin B, Meggio F, Pinna LA: Phosphorylation of calmodulin fragments by protein kinase CK2. Mechanistic aspects and structural consequences. Biochemistry 2004, 43(40):12788-12798.
37. Huang EJ, Reichardt LF: Trk receptors: roles in neuronal signal transduction. Annu Rev Biochem 2003, 72:609-642.