The DOI matches its Crossref record; 27 of the 27 references it cites were found in a registry or an index.
Automated docking with grid‐based energy evaluation
Abstract
The ability to generate feasible binding orientations of a small molecule within a site of known structure is important for ligand design. We present a method that combines a rapid, geometric docking algorithm with the evaluation of molecular mechanics interaction energies. The computational costs of evaluation are minimal because we precalculate the receptor‐dependent terms in the potential function at points on a three‐dimensional grid. In four test cases where the components of crystallographically determined complexes are redocked, the “force field” score correctly identifies the family of orientations closest to the experimental binding geometry. Scoring functions that consider only steric factors or only electrostatic factors are less successful. The force field function will play an important role in our efforts to search databases for potential lead compounds.
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Cites
The protein data bank: A computer-based archival file for macromolecular structures
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977) · Journal of Molecular Biology · doi:10.1016/s0022-2836(77)80200-3 · Cited by 8,578
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. (1984) · Journal of the American Chemical Society · doi:10.1021/ja00315a051 · Cited by 4,639
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
An all atom force field for simulations of proteins and nucleic acids
Weiner, S. J., Kollman, P. A., Nguyen, D. T., & Case, D. A. (1986) · Journal of Computational Chemistry · doi:10.1002/jcc.540070216 · Cited by 3,437
An approach to computing electrostatic charges for molecules
Singh, U. C., & Kollman, P. A. (1984) · Journal of Computational Chemistry · doi:10.1002/jcc.540050204 · Cited by 3,428
Solvent-Accessible Surfaces of Proteins and Nucleic Acids
Connolly, M. L. (1983) · Science · doi:10.1126/science.6879170 · Cited by 2,745
AREAS, VOLUMES, PACKING, AND PROTEIN STRUCTURE
Richards, F. M. (1977) · Annual Review of Biophysics and Bioengineering · doi:10.1146/annurev.bb.06.060177.001055 · Cited by 2,661
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Analytical molecular surface calculation
Connolly, M. L. (1983) · Journal of Applied Crystallography · doi:10.1107/s0021889883010985 · Cited by 2,508
A geometric approach to macromolecule-ligand interactions
Kuntz, I. D., Blaney, J. M., Oatley, S. J., Langridge, R., & Ferrin, T. E. (1982) · Journal of Molecular Biology · doi:10.1016/0022-2836(82)90153-x · Cited by 2,278
Self-citation
Cited by
Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery
Meng, X.-Y., Zhang, H.-X., Mezei, M., & Cui, M. (2011) · Current Computer Aided-Drug Design · doi:10.2174/157340911795677602 · Cited by 3,771
Benchmarking sets for molecular docking.
Huang, N., Shoichet, B. K., & Irwin, J. J. (2006) · Journal of Medicinal Chemistry · doi:10.1021/jm0608356 · Cited by 1,318
Self-citationUltra-large library docking for discovering new chemotypes
Lyu, J., Wang, S., Balius, T. E., Singh, I., Levit, A., Moroz, Y. S., O’Meara, M. J., Che, T., Algaa, E., Tolmachova, K., et al. (2019) · Nature · doi:10.1038/s41586-019-0917-9 · Cited by 998
Self-citationMahley, R. W., Weisgraber, K. H., & Huang, Y. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0600549103 · Cited by 912
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 788
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Metadata
- Authors
- Meng, E. C., Shoichet, B. K., & Kuntz, I. D.
- Venue
- Journal of Computational Chemistry
- Publisher
- Wiley
- Published
- 1992-05
- Volume
- 13
- Issue
- 4
- Pages
- 505-524
- ISSN
- 0192-8651 (ISSN-L)
- 1096-987X
- OpenAlex
- W2171234651
- Cited by
- 938
- References
- 27
- FWCI
- 26.99
- Type
- journal article
- Language
- en
- Open access
- closed
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- Meng, E. C., Shoichet, B. K., & Kuntz, I. D. (1992). Automated docking with grid‐based energy evaluation. Journal of Computational Chemistry. https://doi.org/10.1002/jcc.540130412
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
