A semiempirical free energy force field with charge‐based desolvation

TLDR

The authors develop and test a semiempirical free‑energy force field for use in AutoDock4 and related grid‑based docking methods. The force field combines a comprehensive thermodynamic model that incorporates intramolecular energies with a charge‑based desolvation scheme, calibrated on 188 diverse protein–ligand complexes and validated on 100 retroviral protease complexes. Redocking simulations show the new force field outperforms the previous AutoDock3 force field. © 2007 Wiley Periodicals, Inc., J Comput Chem.

Abstract

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, 2007