Prediction of protein-protein interaction sites using patch-based residue characterization

J Theor Biol. 2012 Jan 21;293:143-50. doi: 10.1016/j.jtbi.2011.10.021. Epub 2011 Oct 25.

Abstract

Identifying protein-protein interaction sites provides important clues to the function of a protein and is becoming increasingly relevant in topics such as systems biology and drug discovery. Using a patch-based model for residue characterization, we trained random forest classifiers for residue-based interface prediction, which was followed by a clustering procedure to produce patches for patch-based interface prediction. For residue-based interface prediction, our method achieves a specificity rate of 0.7 and a sensitivity rate of 0.78. For patch-based interface prediction, a success rate of 0.80 is achieved. Based on same datasets, we also compare it with several published methods. The results show that our method is a successful predictor for residue-based and patch-based interface prediction.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Binding Sites
  • Cluster Analysis
  • Computational Biology / methods
  • Databases, Protein
  • Models, Molecular*
  • Protein Binding
  • Protein Interaction Domains and Motifs*
  • Protein Interaction Mapping / methods*