Computational analysis on similarity of binding pockets in proteins

Electronic-Structure Informatics analysis on the FMO-based fragment interaction analysis

Abstract

We study the spatial distribution of amino acid residues that strongly interact with a ligand bound to the binding pocket of a protein. This analysis is based on the fragment molecular orbital (FMO) calculations. Taking the binding pocket of the protein as the center, we develop a method where the binding pocket was numerically evaluated on the basis of results from FMO calculations. By using the newly developed method, homology of different ligands and binding pockets are analyzed for characterization and classification.