title: KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns.
abstract: Due to the importance of protein phosphorylation in cellular control, many researches are undertaken to predict the kinase-specific phosphorylation sites. Referred to our previous work, KinasePhos 1.0, incorporated profile hidden Markov model (HMM) with flanking residues of the kinase-specific phosphorylation sites. Herein, a new web server, KinasePhos 2.0, incorporates support vector machines (SVM) with the protein sequence profile and protein coupling pattern, which is a novel feature used for identifying phosphorylation sites. The coupling pattern [XdZ] denotes the amino acid coupling-pattern of amino acid types X and Z that are separated by d amino acids. The differences or quotients of coupling strength C(XdZ) between the positive set of phosphorylation sites and the background set of whole protein sequences from Swiss-Prot are computed to determine the number of coupling patterns for training SVM models. After the evaluation based on k-fold cross-validation and Jackknife cross-validation, the average predictive accuracy of phosphorylated serine, threonine, tyrosine and histidine are 90, 93, 88 and 93%, respectively. KinasePhos 2.0 performs better than other tools previously developed. The proposed web server is freely available at http://KinasePhos2.mbc.nctu.edu.tw/.
authors.affiliation: Institute of Bioinformatics, National Chiao Tung University, Hsin-chu 300, Taiwan.
authors.forename: Yung-Hao
authors.initials: YH
authors.lastname: Wong
authors.forename: Tzong-Yi
authors.initials: TY
authors.lastname: Lee
authors.forename: Han-Kuen
authors.initials: HK
authors.lastname: Liang
authors.forename: Chia-Mao
authors.initials: CM
authors.lastname: Huang
authors.forename: Ting-Yuan
authors.initials: TY
authors.lastname: Wang
authors.forename: Yi-Huan
authors.initials: YH
authors.lastname: Yang
authors.forename: Chia-Huei
authors.initials: CH
authors.lastname: Chu
authors.forename: Hsien-Da
authors.initials: HD
authors.lastname: Huang
authors.forename: Ming-Tat
authors.initials: MT
authors.lastname: Ko
authors.forename: Jenn-Kang
authors.initials: JK
authors.lastname: Hwang
mesh_terms: D020134:Catalytic Domain; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D020407:Internet; D008390:Markov Chains; D016571:Neural Networks, Computer; D010750:Phosphoproteins / Q000737:chemistry* / Q000378:metabolism; D010766:Phosphorylation; D011336:Probability; D011494:Protein Kinases / Q000378:metabolism*; D012680:Sensitivity and Specificity; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D010750:Phosphoproteins; D011494:Protein Kinases