The effect of different electrostatic potentials on docking accuracy: A case study using DOCK5.4

Keng Chang Tsai, Sheng Hung Wang, Nai Wan Hsiao, Minyong Li, Binghe Wang

Research output: Contribution to journalArticle

25 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)3509-3512
Number of pages4
JournalBioorganic and Medicinal Chemistry Letters
Volume18
Issue number12
DOIs
Publication statusPublished - 2008 Jun 15

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All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Medicine
  • Molecular Biology
  • Pharmaceutical Science
  • Drug Discovery
  • Clinical Biochemistry
  • Organic Chemistry

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