Protein Docking

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Among the many recent advances in bioinformatics is the rapid accumulation of 3D structures of protein complexes through X-ray crystallization. These structures provide many insights on protein-protein interactions, facilitating rational drug development and the treatment of disease. However, not all protein complexes have been crystallized, so various computational techniques have been developed to address this situation. One of the most promising approaches is protein docking, where the structure of a complex between two proteins is predicted based on the independently crystallized structures of the components.

We have developed several protein docking algorithms. These include:

  • ZDOCK: Performs a full rigid-body search of docking orientations between two proteins. The current version, 3.0.2, includes performance optimization and a novel pairwise statistical energy potential.
  • M-ZDOCK: A modification of ZDOCK to predict symmetric assemblies using the structure of a subunit.
  • ZRANK: A docking refinement program developed to provide fast and accurate rescoring of models from initial-stage docking (e.g. from ZDOCK), as well as refined docking models (e.g. from RosettaDock).
  • RDOCK: An older docking refinement protocol that utilizes structural minimization and rescoring of initial-stage docking models.
All software is freely available to academic users at this site.

We additionally have several resources available to the community:

  • Benchmark: We have assembled a protein-protein docking benchmark, now in its fourth version with 176 test cases. More information here.
  • ZDOCK Server: We maintain a protein docking server, permitting users to run the latest versions of ZDOCK.
  • Decoy Sets: To facilitate the development and testing of docking algorithms, sets of ZDOCK predictions are available for the most recent version of the docking benchmark.
In addition to the docking benchmark, superior performance of ZDOCK and ZRANK has been demonstrated in a community-wide protein docking blind test, CAPRI. Check this out for more details. For basic information on running ZDOCK, see this site.

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