The DOI matches its Crossref record; 21 of the 21 references it cites were found in a registry or an index.
A semiempirical free energy force field with charge‐based desolvation
Open accessAbstract
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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“The standard force field includes the following terms (eq 1):371where the free energy of binding (FEB) is calculated as a sum of van der Waals (vdW), hydrogen bond (Hbond), Coulomb electrostatic (Elec), desolvation (desolv) and ligand torsional entropy (torsDoF); each term is weighted by a specific value (Wterm) estimated using a linear regression model.37”
From AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins (2014) · cites this paper as [37]
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“Also, in the Gasteiger38 charge model used in AutoDock,37 oxygen atoms are systematically assigned a more negative charge than nitrogen and sulfur, thus resulting in the preferred candidates for chelating positively charged metal.”
From AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins (2014) · cites this paper as [37]
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“Similar to all other pairwise interactions in the force field, the interaction between ligand atoms and metals contained in the receptor is described mainly by van der Waals (ΔHvdW) and Coulomb electrostatic (ΔHelec) terms and, to a smaller degree, by the desolvation term (ΔGdesolv).”
From AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins (2014) · cites this paper as [37]
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Cites
A new force field for molecular mechanical simulation of nucleic acids and proteins
Weiner, S. J., Kollman, P. A., Case, D. A., Singh, U. C., Ghio, C., Alagona, G., Profeta, S., & Weiner, P. K. (1984) · Journal of the American Chemical Society · doi:10.1021/ja00315a051 · Cited by 4,641
Docking and scoring in virtual screening for drug discovery: methods and applications
Kitchen, D. B., Decornez, H. Y., Furr, J. R., & Bajorath, J. (2004) · Nature Reviews Drug Discovery · doi:10.1038/nrd1549 · Cited by 4,354
Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges
Gasteiger, J., & Marsili, M. (1980) · Tetrahedron · doi:10.1016/0040-4020(80)80168-2 · Cited by 4,157
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Virtual Computational Chemistry Laboratory – Design and Description
Tetko, I. V., Gasteiger, J., Todeschini, R., Mauri, A., Livingstone, D. J., Ertl, P., Palyulin, V. A., Radchenko, E. V., Zefirov, N. S., Makarenko, A. S., et al. (2005) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-005-8694-y · Cited by 1,504
Principles of docking: An overview of search algorithms and a guide to scoring functions
Halperin, I., Ma, B., Wolfson, H., & Nussinov, R. (2002) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10115 · Cited by 1,294
Protein–ligand docking: Current status and future challenges
Sousa, S. F., Fernandes, P. A., & Ramos, M. J. (2006) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21082 · Cited by 1,047
Molecular Recognition and Docking Algorithms
Brooijmans, N., & Kuntz, I. D. (2003) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.32.110601.142532 · Cited by 812
A review of protein-small molecule docking methods
Taylor, R. D., Jewsbury, P. J., & Essex, J. W. (2002) · Journal of Computer-Aided Molecular Design · doi:10.1023/a:1020155510718 · Cited by 685
Wang, W., Donini, O., Reyes, C. M., & Kollman, P. A. (2001) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.30.1.211 · Cited by 549
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AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009) · Journal of Computational Chemistry · doi:10.1002/jcc.21256 · Cited by 26,294
Self-citationAutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings
Eberhardt, J., Santos‐Martins, D., Tillack, A. F., & Forli, S. (2021) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c00203 · Cited by 8,292
Computational protein-ligand docking and virtual drug screening with the AutoDock suite
Forli, S., Huey, R., Pique, M. E., Sanner, M. F., Goodsell, D., & Olson, A. (2016) · Nature Protocols · doi:10.1038/nprot.2016.051 · Cited by 2,536
Self-citationLigand docking and binding site analysis with PyMOL and Autodock/Vina
Seeliger, D., & de Groot, B. L. (2010) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-010-9352-6 · Cited by 2,648
SwissParam: A fast force field generation tool for small organic molecules
Zoete, V., Cuendet, M. A., Grosdidier, A., & Michielin, O. A. (2011) · Journal of Computational Chemistry · doi:10.1002/jcc.21816 · Cited by 2,411
Metadata
- Authors
- Huey, R., Morris, G. M., Olson, A. J., & Goodsell, D. S.
- Affiliations
- Scripps Research Institute (US)
- Corresponding author
- 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
- 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
- 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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