In this work we show the applicability of a structural clustering in a molecular docking calculations. Our hierarchical clustering protocol is able to distinguish between correct and incorrect geometry of a ligand interacting with a receptor. For a test case (PDB code 1CKA) we generated multiple models of protein-ligand complexes. High resolution reduced model of protein conformational space was used for fully flexible ligand docking. In these models we observed different mutual orientations between the molecules. However, the most populated cluster exhibited the lowest distance from the crystal structure. This opens new possibilities in structure-based rational drug design and studies of macromolecular assemblies.

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1. Characterization of protein structural changes: an efficient modeling approach.
2. Protein modeling in silico: providing new targets for a drug design