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Prediction of Protein Phosphorylation Sites by Integrating Secondary Structure Information and Other One-Dimensional Structural Properties

Protocol
First Online:
Part of the Methods in Molecular Biology book series (MIMB, volume 1484)

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.

Key words

Phosphorylation site prediction Non-kinase-specific tool Support vector machine 
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Notes

Acknowledgement

This project was supported by funding under CZ’s startup funds from University of Nebraska, Lincoln, NE. This work was completed utilizing the Holland Computing Center of the University of Nebraska.

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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  1. 1.School of Biological SciencesUniversity of Nebraska–LincolnLincolnUSA

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