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Nucleic Acids Res. 2015 Jul 1;43(W1):W356-61. doi: 10.1093/nar/gkv368. Epub 2015 Apr 20.

pyDockSAXS: protein-protein complex structure by SAXS and computational docking.

Author information

1
Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, 08034 Barcelona, Spain.
2
Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
3
European Molecular Biology Laboratory, Hamburg Outstation, 22603 Hamburg, Germany.
4
Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université Montpellier 1 and 2, F-34090 Montpellier, France.
5
Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, 08034 Barcelona, Spain juanf@bsc.es.

Abstract

Structural characterization of protein-protein interactions at molecular level is essential to understand biological processes and identify new therapeutic opportunities. However, atomic resolution structural techniques cannot keep pace with current advances in interactomics. Low-resolution structural techniques, such as small-angle X-ray scattering (SAXS), can be applied at larger scale, but they miss atomic details. For efficient application to protein-protein complexes, low-resolution information can be combined with theoretical methods that provide energetic description and atomic details of the interactions. Here we present the pyDockSAXS web server (http://life.bsc.es/pid/pydocksaxs) that provides an automatic pipeline for modeling the structure of a protein-protein complex from SAXS data. The method uses FTDOCK to generate rigid-body docking models that are subsequently evaluated by a combination of pyDock energy-based scoring function and their capacity to describe SAXS data. The only required input files are structural models for the interacting partners and a SAXS curve. The server automatically provides a series of structural models for the complex, sorted by the pyDockSAXS scoring function. The user can also upload a previously computed set of docking poses, which opens the possibility to filter the docking solutions by potential interface residues or symmetry restraints. The server is freely available to all users without restriction.

PMID:
25897115
PMCID:
PMC4489248
DOI:
10.1093/nar/gkv368
[Indexed for MEDLINE]
Free PMC Article

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