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Template-based protein–protein docking exploiting pairwise interfacial residue restraints
Briefings in Bioinformatics
  • Li C. Xue, Utrecht University
  • João P.G.L.M. Rodrigues, Stanford University
  • Drena Dobbs, Iowa State University
  • Vasant Honavar, The Pennsylvania State University
  • Alexandre M.J.J. Bonvin, Utrecht University
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Although many advanced and sophisticated ab initio approaches for modeling protein–protein complexes have been proposed in past decades, template-based modeling (TBM) remains the most accurate and widely used approach, given a reliable template is available. However, there are many different ways to exploit template information in the modeling process. Here, we systematically evaluate and benchmark a TBM method that uses conserved interfacial residue pairs as docking distance restraints [referred to as alpha carbon–alpha carbon (CA-CA)-guided docking]. We compare it with two other template-based protein–protein modeling approaches, including a conserved non-pairwise interfacial residue restrained docking approach [referred to as the ambiguous interaction restraint (AIR)-guided docking] and a simple superposition-based modeling approach. Our results show that, for most cases, the CA-CA-guided docking method outperforms both superposition with refinement and the AIR-guided docking method. We emphasize the superiority of the CA-CA-guided docking on cases with medium to large conformational changes, and interactions mediated through loops, tails or disordered regions. Our results also underscore the importance of a proper refinement of superimposition models to reduce steric clashes. In summary, we provide a benchmarked TBM protocol that uses conserved pairwise interface distance as restraints in generating realistic 3D protein–protein interaction models, when reliable templates are available. The described CA-CA-guided docking protocol is based on the HADDOCK platform, which allows users to incorporate additional prior knowledge of the target system to further improve the quality of the resulting models.


This article is from Briefings in Bioinformatics (2016), doi: 10.1093/bib/bbw027. Posted with permission.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (, which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Li C. Xue, João P.G.L.M. Rodrigues, Drena Dobbs, Vasant Honavar, et al.. "Template-based protein–protein docking exploiting pairwise interfacial residue restraints" Briefings in Bioinformatics (2016) p. 1 - 9
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