Accuracy of binding mode prediction with a cascadic stochastic tunneling method.
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.
Fischer
Bernhard
B
Forschungszentrum Karlsruhe, Institut für Nanotechnologie, Postfach 3640, D-76021 Karlsruhe, Germany.
Basili
Serena
S
Merlitz
Holger
H
Wenzel
Wolfgang
W
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*
D008024:Ligands; D046912:Multiprotein Complexes; D011506:Proteins