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Accounting for observed small angle X‐ray scattering profile in the protein–protein docking server cluspro
Author(s) -
Xia Bing,
Mamonov Artem,
Leysen Seppe,
Allen Karen N.,
Strelkov Sergei V.,
Paschalidis Ioannis Ch.,
Vajda Sandor,
Kozakov Dima
Publication year - 2015
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.23952
Subject(s) - small angle x ray scattering , docking (animal) , scattering , computer science , small angle scattering , biological system , physics , biology , optics , medicine , nursing
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.