Software news and update a semiempirical free energy force field with charge-based desolvation

Ruth Huey, Garrett M. Morris, Arthur J. Olson, David S. Goodsell

Research output: Contribution to journalArticle

1437 Scopus citations

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 incorpo-rates 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 AutoDockS force field.

Original languageEnglish (US)
Pages (from-to)1145-1152
Number of pages8
JournalJournal of Computational Chemistry
Volume28
Issue number6
DOIs
StatePublished - Apr 30 2007
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Safety, Risk, Reliability and Quality

Keywords

  • AutoDock4
  • Computational docking
  • Computer-aided drug design
  • Desolvation models
  • Force fields
  • Prediction of free energy

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