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Can I perform protein-protein docking with Schrodinger software?

Yes. 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 more information, see Protein-Protein Docking and Docking 1ba7 to 1qqu for a tutorial introduction.

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.

Keywords: rotatable bonds

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