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

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

Research output: Contribution to journalArticle

1349 Citations (Scopus)

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

Fingerprint

Force Field
Free energy
Free Energy
Update
Ligands
Charge
Software
Binding energy
Peptide Hydrolases
Thermodynamics
Proteins
Atoms
Docking
Protease
Binding Energy
Testing
Grid
Protein
Evaluation
Energy

All Science Journal Classification (ASJC) codes

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

Cite this

Huey, Ruth ; Morris, Garrett M. ; Olson, Arthur J. ; Goodsell, David. / Software news and update a semiempirical free energy force field with charge-based desolvation. In: Journal of Computational Chemistry. 2007 ; Vol. 28, No. 6. pp. 1145-1152.
@article{008f34e22dd04f5da73e649e52d93f3a,
title = "Software news and update a semiempirical free energy force field with charge-based desolvation",
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.",
author = "Ruth Huey and Morris, {Garrett M.} and Olson, {Arthur J.} and David Goodsell",
year = "2007",
month = "4",
day = "30",
doi = "10.1002/jcc.20634",
language = "English (US)",
volume = "28",
pages = "1145--1152",
journal = "Journal of Computational Chemistry",
issn = "0192-8651",
publisher = "John Wiley and Sons Inc.",
number = "6",

}

Software news and update a semiempirical free energy force field with charge-based desolvation. / Huey, Ruth; Morris, Garrett M.; Olson, Arthur J.; Goodsell, David.

In: Journal of Computational Chemistry, Vol. 28, No. 6, 30.04.2007, p. 1145-1152.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Software news and update a semiempirical free energy force field with charge-based desolvation

AU - Huey, Ruth

AU - Morris, Garrett M.

AU - Olson, Arthur J.

AU - Goodsell, David

PY - 2007/4/30

Y1 - 2007/4/30

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=33947716119&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33947716119&partnerID=8YFLogxK

U2 - 10.1002/jcc.20634

DO - 10.1002/jcc.20634

M3 - Article

VL - 28

SP - 1145

EP - 1152

JO - Journal of Computational Chemistry

JF - Journal of Computational Chemistry

SN - 0192-8651

IS - 6

ER -