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J Comput Chem. 2007 Apr 30;28(6):1145-52.

A semiempirical free energy force field with charge-based desolvation.

Author information

1
Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92102, USA.

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.

PMID:
17274016
DOI:
10.1002/jcc.20634
[Indexed for MEDLINE]

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