How to use not-always-reliable binding site information in protein-protein docking prediction

PLoS One. 2013 Oct 4;8(10):e75936. doi: 10.1371/journal.pone.0075936. eCollection 2013.

Abstract

In many protein-protein docking algorithms, binding site information is used to help predicting the protein complex structures. Using correct and accurate binding site information can increase protein-protein docking success rate significantly. On the other hand, using wrong binding sites information should lead to a failed prediction, or, at least decrease the success rate. Recently, various successful theoretical methods have been proposed to predict the binding sites of proteins. However, the predicted binding site information is not always reliable, sometimes wrong binding site information could be given. Hence there is a high risk to use the predicted binding site information in current docking algorithms. In this paper, a softly restricting method (SRM) is developed to solve this problem. By utilizing predicted binding site information in a proper way, the SRM algorithm is sensitive to the correct binding site information but insensitive to wrong information, which decreases the risk of using predicted binding site information. This SRM is tested on benchmark 3.0 using purely predicted binding site information. The result shows that when the predicted information is correct, SRM increases the success rate significantly; however, even if the predicted information is completely wrong, SRM only decreases success rate slightly, which indicates that the SRM is suitable for utilizing predicted binding site information.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Binding Sites
  • Protein Binding
  • Protein Structure, Secondary
  • Proteins / chemistry*
  • Proteins / metabolism*

Substances

  • Proteins

Grants and funding

This work is supported by the National Science Foundation of China (www.nsfc.gov.cn) under Grant No. 11174093 and 11074084. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.