FireDock: Fast interaction refinement in molecular docking

Abstract Here, we present FireDock, an efficient method for the refinement and rescoring of rigid‐body docking solutions. The refinement process consists of two main steps: (1) rearrangement of the interface side‐chains and (2) adjustment of the relative orientation of the molecules. Our method accounts for the observation that most interface residues that are important in recognition and binding do not change their conformation significantly upon complexation. Allowing full side‐chain flexibility, a common procedure in refinement methods, often causes excessive conformational changes. These changes may distort preformed structural signatures, which have been shown to be important for binding recognition.…

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