We are interested in determining the binding mode of Sansalvamide A derivatives to the protein Hsp90, which is a promising target in cancer treatment, but conventional crystallography methods have not been successful. Docking software is capable of finding multiple binding modes of a ligand within a protein pocket, but the standard error of force field energy calculations makes it difficult to confidently determine the correct binding mode. A computational method to gain confidence in docking results, multi-compound clustering, is developed and validated against a well-defined data set of pyrazolo[1,5-a][1,3,5]triazine derivatives bound to Casein Kinase 2 (CK2). The clustering methodology is then applied Sansalvamide A derivatives docked to Hsp90.
