title: Prediction of Protein Phosphorylation Sites by Integrating Secondary Structure Information and Other One-Dimensional Structural Properties.
abstract: Studies on phosphorylation are important but challenging for both wet-bench experiments and computational studies, and accurate non-kinase-specific prediction tools are highly desirable for whole-genome annotation in a wide variety of species. Here, we describe a phosphorylation site prediction webserver, PhosphoSVM, that employs Support Vector Machine to combine protein secondary structure information and seven other one-dimensional structural properties, including Shannon entropy, relative entropy, predicted protein disorder information, predicted solvent accessible area, amino acid overlapping properties, averaged cumulative hydrophobicity, and subsequence k-nearest neighbor profiles. This method achieved AUC values of 0.8405/0.8183/0.7383 for serine (S), threonine (T), and tyrosine (Y) phosphorylation sites, respectively, in animals with a tenfold cross-validation. The model trained by the animal phosphorylation sites was also applied to a plant phosphorylation site dataset as an independent test. The AUC values for the independent test data set were 0.7761/0.6652/0.5958 for S/T/Y phosphorylation sites, respectively. This algorithm with the optimally trained model was implemented as a webserver. The webserver, trained model, and all datasets used in the current study are available at http://sysbio.unl.edu/PhosphoSVM .
authors: School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-0118, USA.
authors: Yongchao
authors: Y
authors: Dou
authors: School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-0118, USA.
authors: Bo
authors: B
authors: Yao
authors: School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-0118, USA. czhang5@unl.edu.
authors: Chi
authors: C
authors: Zhang
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence / Q000235:genetics; D000596:Amino Acids / Q000737:chemistry / Q000235:genetics*; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods; D057927:Hydrophobic and Hydrophilic Interactions; D010766:Phosphorylation; D017433:Protein Structure, Secondary / Q000235:genetics*; D011506:Proteins / Q000737:chemistry / Q000235:genetics*
chemical_list: D000596:Amino Acids; D011506:Proteins
keywords: Non-kinase-specific tool; Phosphorylation site prediction; Support vector machine