CANDOCK: Chemical atomic network based hierarchical flexible docking algorithm using generalized statistical potentials

Abstract

Small molecule docking has proven to be invaluable for drug design and discovery. However, existing docking methods have several limitations, such as, improper treatment of the interactions of essential components in the chemical environment of the binding pocket (e.g. cofactors, metal-ions, etc.), incomplete sampling of chemically relevant ligand conformational space, and the inability to consistently correlate docking scores of the best binding pose with experimental binding affinities. We present CANDOCK, a novel docking algorithm that utilizes a hierarchical approach to reconstruct ligands from an atomic grid using graph theory and generalized statistical potential functions to sample biologically relevant ligand conformations. Our algorithm accounts for protein flexibility, solvent, metal ions and cofactors interactions in the binding pocket that are traditionally ignored by current methods. We evaluate the algorithm on the PDBbind and Astex proteins to show its ability to reproduce the binding mode of the ligands that is independent of the initial ligand conformation in these benchmarks. Finally, we identify the best selector and ranker potential functions, such that, the statistical score of best selected docked pose correlates with the experimental binding affinities of the ligands for any given protein target. Our results indicate that CANDOCK is a generalized flexible docking method that addresses several limitations of current docking methods by considering all interactions in the chemical environment of a binding pocket for correlating the best docked pose with biological activity.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=28 SRC=\"FIGDIR/small/442897v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (16K):\norg.highwire.dtl.DTLVardef@1c1b2b0org.highwire.dtl.DTLVardef@1ba66a4org.highwire.dtl.DTLVardef@a8bfd3org.highwire.dtl.DTLVardef@c9d3bb_HPS_FORMAT_FIGEXP M_FIG C_FIG