The effect of different electrostatic potentials on docking accuracy: a case study using DOCK5.4.
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.
Tsai
Keng-Chang
KC
The Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan.
Wang
Sheng-Hung
SH
Hsiao
Nai-Wan
NW
Li
Minyong
M
Wang
Binghe
B
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
D008024:Ligands