Prediction of Protein-compound Complex Structures by Docking Simulation

Abstract

Protein-compound docking is a key technology in structure-guided drug development (SGDD), and some combinations of computational methods including the protein-compound docking have been used in the SGDD. Ligand-binding site prediction is the first step in the SGDD. The second step is the ensemble docking, in which compounds in a database are docked onto the protein surfaces of a structural ensemble of the target protein. The third step is the information analysis of the docking results. Finally, suitable docking results are selected for an assay experiment. Topics around the protein-compound docking and the SGDD are briefly explained.