title: Accounting for observed small angle X-ray scattering profile in the protein-protein docking server ClusPro.
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.
authors.affiliation: Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts, 02215.
authors.forename: Bing
authors.initials: B
authors.lastname: Xia
authors.affiliation: Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts, 02215.
authors.forename: Artem
authors.initials: A
authors.lastname: Mamonov
authors.affiliation: Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium.
authors.forename: Seppe
authors.initials: S
authors.lastname: Leysen
authors.affiliation: Department of Chemistry, Boston University, Boston, Massachusetts, 02215.
authors.forename: Karen N
authors.initials: KN
authors.lastname: Allen
authors.affiliation: Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium.
authors.forename: Sergei V
authors.initials: SV
authors.lastname: Strelkov
authors.affiliation: Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, 02215.
authors.forename: Ioannis Ch
authors.initials: ICh
authors.lastname: Paschalidis
authors.affiliation: Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts, 02215.
authors.forename: Sandor
authors.initials: S
authors.lastname: Vajda
authors.affiliation: Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts, 02215.
authors.forename: Dima
authors.initials: D
authors.lastname: Kozakov
mesh_terms: D062105:Molecular Docking Simulation; D011506:Proteins / Q000737:chemistry*; D053838:Scattering, Small Angle; D014961:X-Ray Diffraction
chemical_list: D011506:Proteins
keywords: docking method; protein complex; scoring function; small angle X-ray scattering restraints; structure prediction