title: Accuracy of binding mode prediction with a cascadic stochastic tunneling method.
abstract: We investigate the accuracy of the binding modes predicted for 83 complexes of the high-resolution subset of the ASTEX/CCDC receptor-ligand database using the atomistic FlexScreen approach with a simple forcefield-based scoring function. The median RMS deviation between experimental and predicted binding mode was just 0.83 A. Over 80% of the ligands dock within 2 A of the experimental binding mode, for 60 complexes the docking protocol locates the correct binding mode in all of ten independent simulations. Most docking failures arise because (a) the experimental structure clashed in our forcefield and is thus unattainable in the docking process or (b) because the ligand is stabilized by crystal water.
authors.affiliation: Forschungszentrum Karlsruhe, Institut für Nanotechnologie, Postfach 3640, D-76021 Karlsruhe, Germany.
authors.forename: Bernhard
authors.initials: B
authors.lastname: Fischer
authors.forename: Serena
authors.initials: S
authors.lastname: Basili
authors.forename: Holger
authors.initials: H
authors.lastname: Merlitz
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Wenzel
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D008024:Ligands; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000737:chemistry*; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry*
chemical_list: D008024:Ligands; D046912:Multiprotein Complexes; D011506:Proteins