期刊
JOURNAL OF COMPUTATIONAL CHEMISTRY
卷 28, 期 6, 页码 1145-1152出版社
JOHN WILEY & SONS INC
DOI: 10.1002/jcc.20634
关键词
computational docking; prediction of free energy; force fields; desolvation models; computer-aided drug design; AutoDock4
资金
- NIGMS NIH HHS [P01 GM48870, R01 GM069832] Funding Source: Medline
The authors describe the development and testing of a semiempirical free energy force field for use in AutoDock4 and similar grid-based docking methods. The force field is based on a comprehensive thermodynamic model that allows incorporation of intramolecular energies into the predicted free energy of binding. It also incorporates a charge-based method for evaluation of desolvation designed to use a typical set of atom types. The method has been calibrated on a set of 188 diverse protein-ligand complexes of known structure and binding energy, and tested on a set of 100 complexes of ligands with retroviral proteases. The force field shows improvement in redocking simulations over the previous AutoDock3 force field. (C) 2007 Wiley Periodicals, Inc.
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