A semiempirical free energy force field with charge‐based desolvation
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Open Access
- 1 February 2007
- journal article
- research article
- Published by Wiley in Journal of Computational Chemistry
- Vol. 28 (6) , 1145-1152
- https://doi.org/10.1002/jcc.20634
Abstract
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. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007Keywords
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