RosettaLigand docking with full ligand and receptor flexibility.

Computational docking of small-molecule ligands into protein receptors is an important tool for modern drug discovery. Although conformational adjustments are frequently observed between the free and ligand-bound states, the conformational flexibility of the protein is typically ignored in protein-small molecule docking programs. We previously described the program RosettaLigand, which leverages the Rosetta energy function and side-chain repacking algorithm to account for flexibility of all side chains in the binding site. Here we present extensions to RosettaLigand that incorporate full ligand flexibility as well as receptor backbone flexibility. Including receptor backbone flexibility is found to produce more correct docked complexes and to lower the average RMSD of the best-scoring docked poses relative to the rigid-backbone results. On a challenging set of retrospective and prospective cross-docking tests, we find that the top-scoring ligand pose is correctly positioned within 2 A RMSD for 64% (54/85) of cases overall.