Cited by 2,246Computational Drug Discovery MethodsAdvanced Chemical Physics StudiesProtein Structure and Dynamics

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A semiempirical free energy force field with charge‐based desolvation

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Huey, Ruth, Morris, Garrett M., Olson, Arthur J., Goodsell, David S.·2007·Journal of Computational Chemistry

DOI 10.1002/jcc.20634

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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

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Authors: Huey, R., Morris, G. M., Olson, A. J., & Goodsell, D. S.
Affiliations: Scripps Research Institute (US)
Corresponding author: Goodsell, David S.
ORCID: Morris, Garrett M.
Olson, Arthur J.
Goodsell, David S.
Venue: Journal of Computational Chemistry
Publisher: Wiley
Published: 2007-02
Volume: 28
Issue: 6
Pages: 1145-1152
ISSN: 0192-8651 (ISSN-L)
1096-987X
DOI: 10.1002/jcc.20634
OpenAlex: W2165526004
Cited by: 2,246
References: 21
Citations by year: 2026: 80 · 2025: 105 · 2024: 115 · 2023: 110 · 2022: 116 · 2021: 114 · 2020: 127 · 2019: 132 · 2018: 112 · 2017: 126 · 2016: 121 · 2015: 108 · 2014: 116 · 2013: 135 · 2012: 151
FWCI: 130.12
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: onlinelibrary.wiley.com/termsAndConditions#vor (vor)
Locations: Journal of Computational Chemistry (publishedVersion)
PubMed (publishedVersion)
Funders: National Institutes of Health
National Institute of General Medical Sciences (P01GM048870, P01 GM48870, R01GM069832)
Topics: Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Advanced Chemical Physics Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords: protein-ligand docking, desolvation, binding free energy, retroviral protease, redocking, force field calibration
MeSH terms: Algorithms, Hydrogen Bonding, Ligands, Mathematical Computing, Models, Chemical, Models, Molecular, Molecular Conformation, Protein Binding, Proteins, Software, Thermodynamics, Water, Drug Design, HIV Protease, HIV Protease Inhibitors, Databases, Protein, Static Electricity

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A semiempirical free energy force field with charge‐based desolvation

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