Article ID | Journal | Published Year | Pages | File Type |
---|---|---|---|---|
1376334 | Bioorganic & Medicinal Chemistry Letters | 2008 | 4 Pages |
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.
Graphical abstractNine different semi-empirical and empirical charges were compared their performance on the prediction of docking poses using DOCK5.4 program.Figure optionsDownload full-size imageDownload as PowerPoint slide