A semiempirical free energy force field with charge-based desolvation

J Comput Chem. 2007 Apr 30;28(6):1145-52. doi: 10.1002/jcc.20634.


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • Databases, Protein
  • Drug Design
  • HIV Protease / chemistry
  • HIV Protease / metabolism
  • HIV Protease Inhibitors / chemistry
  • Hydrogen Bonding
  • Ligands
  • Mathematical Computing
  • Models, Chemical*
  • Models, Molecular
  • Molecular Conformation
  • Protein Binding
  • Proteins / chemistry*
  • Proteins / metabolism
  • Software
  • Static Electricity
  • Thermodynamics*
  • Water / chemistry


  • HIV Protease Inhibitors
  • Ligands
  • Proteins
  • Water
  • HIV Protease