Acta Phys. -Chim. Sin. ›› 2012, Vol. 28 ›› Issue (04): 751-758.doi: 10.3866/PKU.WHXB201202022

• REVIEW • Previous Articles     Next Articles

Progress in the Scoring Functions of Protein-Protein Docking

WANG Cun-Xin1, CHANG Shan2, GONG Xin-Qi3, YANG Feng1, LI Chun-Hua1, CHEN Wei-Zu1   

  1. 1. College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, P. R. China;
    2. College of Informatics, South China Agricultural University, Guangzhou 510642, P. R. China;
    3. School of Life Sciences, Tsinghua University, Beijing 100084, P. R. China
  • Received:2011-11-22 Revised:2012-01-12 Published:2012-03-21
  • Contact: WANG Cun-Xin
  • Supported by:

    The project was supported by the National Natural Science Foundation of China (10974008, 31171267), Specialized Research Fund for the Doctoral Program of Higher Education, China (200800050003), and International Science & Technology Cooperation Program of China (2010DFA31710).

Abstract: Molecular docking technology is an effective approach for prediction of intermolecular interactions and recognition. The design of a scoring function for selecting near-native structures is very important for successful prediction of complex structures. In this article, the main computational methods for scoring items in protein-protein docking, such as geometric complementarity, contact area, van der Waals' interaction, electrostatic interaction, and statistical pair propensity potential, are reviewed. Including our work, we introduce commonly used scoring schemes and some strategies in screening decoys based on the information for protein binding sites. The characteristic scoring functions in the commonly used docking programs are compared and summarized. The major problems in the existing scoring function in protein-protein docking are discussed along with prospect for future research.

Key words: Protein-protein docking, Scoring function, Scoring scheme, Binding site information