Consensus scoring for enriching near-native structures from protein–protein docking decoys

Authors

  • Shide Liang,

    1. Indiana University School of Informatics, Indiana University-Purdue University, Indianapolis, Indiana 46202
    2. Department of Biochemistry and Molecular Biology and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202
    3. Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
    Search for more papers by this author
  • Samy O. Meroueh,

    1. Department of Biochemistry and Molecular Biology and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202
    Search for more papers by this author
  • Guangce Wang,

    1. Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
    Search for more papers by this author
  • Chao Qiu,

    1. Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
    Search for more papers by this author
  • Yaoqi Zhou

    Corresponding author
    1. Indiana University School of Informatics, Indiana University-Purdue University, Indianapolis, Indiana 46202
    2. Department of Biochemistry and Molecular Biology and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202
    • Indiana University School of Informatics, Indiana University-Purdue University at Indianapolis and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 719 Indiana Ave. Rm 319, Indianapolis, IN 46202
    Search for more papers by this author

Abstract

The identification of near native protein–protein complexes among a set of decoys remains highly challenging. A strategy for improving the success rate of near native detection is to enrich near native docking decoys in a small number of top ranked decoys. Recently, we found that a combination of three scoring functions (energy, conservation, and interface propensity) can predict the location of binding interface regions with reasonable accuracy. Here, these three scoring functions are modified and combined into a consensus scoring function called ENDES for enriching near native docking decoys. We found that all individual scores result in enrichment for the majority of 28 targets in ZDOCK2.3 decoy set and the 22 targets in Benchmark 2.0. Among the three scores, the interface propensity score yields the highest enrichment in both sets of protein complexes. When these scores are combined into the ENDES consensus score, a significant increase in enrichment of near-native structures is found. For example, when 2000 dock decoys are reduced to 200 decoys by ENDES, the fraction of near-native structures in docking decoys increases by a factor of about six in average. ENDES was implemented into a computer program that is available for download at http://sparks.informatics.iupui.edu. Proteins 2009. © 2008 Wiley-Liss, Inc.

Ancillary