title: The effect of different electrostatic potentials on docking accuracy: a case study using DOCK5.4.
abstract: As a commonly used structure-based approach for virtual screening, molecular design and lead optimization, molecular docking can search the preferred orientation and conformation of a ligand for its optimal binding to a receptor or enzyme active site. In doing so, selecting an appropriate method to calculate the electrostatic potentials is critical. In the current report, nine different semi-empirical and empirical methods, including AM1, AM1-BCC, Del-Re, MMFF, Gasteiger, Hückel, Gasteiger-Hückel, Pullman and formal charges were investigated for their performance on the prediction of docking poses using the DOCK5.4 program. The results demonstrated that the AM1-BCC charges had the highest success rate.
authors.affiliation: The Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan.
authors.forename: Keng-Chang
authors.initials: KC
authors.lastname: Tsai
authors.forename: Sheng-Hung
authors.initials: SH
authors.lastname: Wang
authors.forename: Nai-Wan
authors.initials: NW
authors.lastname: Hsiao
authors.forename: Minyong
authors.initials: M
authors.lastname: Li
authors.forename: Binghe
authors.initials: B
authors.lastname: Wang
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D015195:Drug Design; D008024:Ligands; D011237:Predictive Value of Tests; D012984:Software; D055672:Static Electricity; D013329:Structure-Activity Relationship
chemical_list: D008024:Ligands