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Accounting for observed small angle X-ray scattering profile in the protein-protein docking server ClusPro.

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      Abstract

      The protein-protein docking server ClusPro is used by thousands of laboratories, and models built by the server have been reported in over 300 publications. Although the structures generated by the docking include near-native ones for many proteins, selecting the best model is difficult due to the uncertainty in scoring. Small angle X-ray scattering (SAXS) is an experimental technique for obtaining low resolution structural information in solution. While not sufficient on its own to uniquely predict complex structures, accounting for SAXS data improves the ranking of models and facilitates the identification of the most accurate structure. Although SAXS profiles are currently available only for a small number of complexes, due to its simplicity the method is becoming increasingly popular. Since combining docking with SAXS experiments will provide a viable strategy for fairly high-throughput determination of protein complex structures, the option of using SAXS restraints is added to the ClusPro server. © 2015 Wiley Periodicals, Inc.

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      Affiliations
      [1 ] Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts, 02215.
      [2 ] Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium.
      [3 ] Department of Chemistry, Boston University, Boston, Massachusetts, 02215.
      [4 ] Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, 02215.
      Journal
      J Comput Chem
      Journal of computational chemistry
      Wiley-Blackwell
      1096-987X
      0192-8651
      Jul 30 2015
      : 36
      : 20
      26095982
      10.1002/jcc.23952
      4485579
      NIHMS691105

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