Effect of input differences on the results of docking calculations.
The sensitivity of docking calculations to the geometry of the input ligand was studied. It was found that even small changes in the ligand input conformation can lead to large differences in the geometries and scores of the resulting docked poses. The accuracy of docked poses produced from different ligand input structures-the X-ray structure, the minimized Corina structure, and structures generated from conformational searches and molecular dynamics ensembles-were also assessed. It was found that using the X-ray ligand conformation as docking input does not always produce the most accurate docked pose when compared with other sources of ligand input conformations. Furthermore, no one method of conformer generation is guaranteed to always produce the most accurate docking pose. The docking scores are also highly sensitive to the source of the input conformation, which might introduce some noise in compound ranking and in binding affinity predictions. It is concluded that for the purposes of reproducibility and optimal performance, the most prudent procedure is to use multiple input structures for docking. The implications of these results on docking validation studies are discussed.
Feher
Miklos
M
Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto Medical Discovery Tower, 101 College Street, Suite 5-361, Toronto, Ontario M5G 1L7, Canada. mfeher@uhnres.utoronto.ca
Williams
Christopher I
CI
D001665:Binding Sites; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D008968:Molecular Conformation; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D040301:Vascular Endothelial Growth Factor Receptor-2 / Q000737:chemistry / Q000378:metabolism
D008024:Ligands; D011506:Proteins; D040301:Vascular Endothelial Growth Factor Receptor-2