Evaluation of Docking Accuracy and Investigations of Roles of Parameters and Each Term in Scoring Functions for Protein–Ligand Docking Using ArgusLab Software
Akifumi Oda, Megumi Okayasu, Yukiko Kamiyama, Tomoki Yoshida, Ohgi Takahashi, Hisao Matsuzaki · Bulletin of the Chemical Society of Japan · 2007
Abstract We evaluated the docking accuracy of ArgusLab, which is a freely available software program for computational docking, using experimentally determined protein–ligand complex structures. Investigations of the roles of parameters used for docking calculations in ArgusLab were carried out in addition to evaluation of the software. The results indicate that one docking engine of ArgusLab, GADock, is superior in terms of accuracy, and that another docking engine, ArgusDock, is advantageous in terms of the computational time it provides. In a pose construction step, larger population sizes generated more accurate poses using GADock. The docking poses constructed by GADock were easier to evaluate than those of ArgusDock in the pose-selection step. Reliable docking calculations are expected to be carried out with ArgusLab using results of this study.