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Can I perform protein-protein docking with Schrodinger software?

Yes. From Suite 2012, protein-protein docking is supported in the BioLuminate product, which provides an interface to the Piper protein-protein docking program. This program performs rigid docking of two proteins by sampling all possible orientations and scoring the results.

For flexible protein-protein docking, the best approach might be a conformational search with the LLMOD method (large-scale low-mode sampling) in MacroModel. This sampling method is designed to treat large, flexible structures, although you can limit the search to the interaction areas using the substructure feature. You could follow this type of conformational search with Prime side-chain predictions and loop sampling at the protein-protein interface, if needed.

There is also a script available from the Script Center of our web site (Resources & Downloads → Script Center), "Component interactions", in the Molecular Mechanics section, that will allow you to calculate the interaction energies between atom sets.

Keywords: rotatable bonds

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