Principles of flexible protein-protein docking

Nelly Andrusier, Efrat Mashiach, Ruth Nussinov, Haim J. Wolfson

Research output: Contribution to journalReview articlepeer-review


Treating flexibility in molecular docking is a major challenge in cell biology research. Here we describe the background and the principles of existing flexible protein-protein docking methods, focusing on the algorithms and their rational. We describe how protein flexibility is treated in different stages of the docking process: in the preprocessing stage, rigid and flexible parts are identified and their possible conformations are modeled. This preprocessing provides information for the subsequent docking and refinement stages. In the docking stage, an ensemble of pre-generated conformations or the identified rigid domains may be docked separately. In the refinement stage, small-scale movements of the backbone and side-chains are modeled and the binding orientation is improved by rigid-body adjustments. For clarity of presentation, we divide the different methods into categories. This should allow the reader to focus on the most suitable method for a particular docking problem.

Original languageEnglish
Pages (from-to)271-289
Number of pages19
JournalProteins: Structure, Function and Genetics
Issue number2
StatePublished - 1 Nov 2008


  • Backbone flexibility
  • Flexible docking
  • Modeling protein-protein docking
  • Rigid-body optimization
  • Side-chain refinement


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