pyDockSAXS server is a web server for rigid-body protein-protein docking that combines computational and
On one side the server uses the new version of pyDock (pyDock 3.0) to energetically evaluate the interaction surface of multiple docking poses.
On the other side, the server evaluates the capacity of each pose to describe the experimental curve of SAXS with the program CRYSOL. The appropriate combination of both scoring functions yields predictions of the 3D arrangement of the complex in solution.
Please find the details of the method here.
Please cite these references if you use pyDockSAXS server in your research:
pyDockSAXS: protein-protein complex structure by SAXS and computational docking, B Jiménez-García, C Pons, DI. Svergun, P Bernadó and J Fernández-Recio. Nucleic Acids Research 2015; doi: 10.1093/nar/gkv368
Structural Characterization of Protein–Protein Interactions with pyDockSAXS, B Jiménez-García, P Bernadó and J Fernández-Recio. Structural Bioinformatics, 131-144.
How to use it
Receptor PDB and ligand PDB are valid PDB structure files and
their relative positions and orientations are evaluated with pyDockSAXS.
Notice that SAXS is sensitive to the molecular weight of the molecules. If receptor and ligand pdbs are only partial representations of the protein species experimentally measured in the complex bad results will probably derived. The SAXS experimental curve is a CRYSOL compatible file.
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