Prediction of posttranslational modification sites from amino acid sequences with kernel methods

J Theor Biol. 2014 Mar 7;344:78-87. doi: 10.1016/j.jtbi.2013.11.012. Epub 2013 Nov 27.


Post-translational modification (PTM) is the chemical modification of a protein after its translation and one of the later steps in protein biosynthesis for many proteins. It plays an important role which modifies the end product of gene expression and contributes to biological processes and diseased conditions. However, the experimental methods for identifying PTM sites are both costly and time-consuming. Hence computational methods are highly desired. In this work, a novel encoding method PSPM (position-specific propensity matrices) is developed. Then a support vector machine (SVM) with the kernel matrix computed by PSPM is applied to predict the PTM sites. The experimental results indicate that the performance of new method is better or comparable with the existing methods. Therefore, the new method is a useful computational resource for the identification of PTM sites. A unified standalone software PTMPred is developed. It can be used to predict all types of PTM sites if the user provides the training datasets. The software can be freely downloaded from

Keywords: Kinase-specific; O-glycosylation; Phosphorylation; Support vector machine.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acid Sequence / genetics*
  • Animals
  • Computational Biology / methods*
  • Glycosylation
  • Phosphorylation
  • Phosphotransferases / genetics
  • Phosphotransferases / metabolism
  • Position-Specific Scoring Matrices
  • Protein Processing, Post-Translational*
  • Software Design*
  • Support Vector Machine


  • Phosphotransferases