PalmPred: an SVM based palmitoylation prediction method using sequence profile information

PLoS One. 2014 Feb 19;9(2):e89246. doi: 10.1371/journal.pone.0089246. eCollection 2014.

Abstract

Protein palmitoylation is the covalent attachment of the 16-carbon fatty acid palmitate to a cysteine residue. It is the most common acylation of protein and occurs only in eukaryotes. Palmitoylation plays an important role in the regulation of protein subcellular localization, stability, translocation to lipid rafts and many other protein functions. Hence, the accurate prediction of palmitoylation site(s) can help in understanding the molecular mechanism of palmitoylation and also in designing various related experiments. Here we present a novel in silico predictor called 'PalmPred' to identify palmitoylation sites from protein sequence information using a support vector machine model. The best performance of PalmPred was obtained by incorporating sequence conservation features of peptide of window size 11 using a leave-one-out approach. It helped in achieving an accuracy of 91.98%, sensitivity of 79.23%, specificity of 94.30%, and Matthews Correlation Coefficient of 0.71. PalmPred outperformed existing palmitoylation site prediction methods - IFS-Palm and WAP-Palm on an independent dataset. Based on these measures it can be anticipated that PalmPred will be helpful in identifying candidate palmitoylation sites. All the source datasets, standalone and web-server are available at http://14.139.227.92/mkumar/palmpred/.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites / genetics*
  • Conserved Sequence / genetics
  • Lipoylation / physiology*
  • Models, Biological*
  • Proteins / genetics*
  • Proteins / metabolism*
  • Sensitivity and Specificity
  • Software*
  • Support Vector Machine

Substances

  • Proteins

Grant support

Bandana Kumari is supported by a University Grant Commission non-NET fellowship (Non-Net/139/2012) and Ravindra Kumar by a Senior Research fellowship (20-12/2009(ii)EU-IV) from the University Grant Commission of India. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.