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A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
Abstract
The interaction of a probe group with a protein of known structure is computed at sample positions throughout and around the macromolecule, giving an array of energy values. The probes include water, the methyl group, amine nitrogen, carboxy oxygen, and hydroxyl. Contour surfaces at appropriate energy levels are calculated for each probe and displayed by computer graphics together with the protein structure. Contours at negative energy levels delineate contours also enable other regions of attraction between probe and protein and are found at known ligand binding clefts in particular. The contours also enable other regions of attraction to be identified and facilitate the interpretation of protein-ligand energetics. They may, therefore, be of value for drug design.
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Cited by
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Meng, X.-Y., Zhang, H.-X., Mezei, M., & Cui, M. (2011) · Current Computer Aided-Drug Design · doi:10.2174/157340911795677602 · Cited by 3,771
A semiempirical free energy force field with charge‐based desolvation
Huey, R., Morris, G. M., Olson, A. J., & Goodsell, D. S. (2007) · Journal of Computational Chemistry · doi:10.1002/jcc.20634 · Cited by 2,246
QSAR Modeling: Where have you been? Where are you going to?
Cherkasov, A., Muratov, E. N., Fourches, D., Varnek, A., Baskin, I. I., Cronin, M., Dearden, J., Gramatica, P., Martin, Y. C., Todeschini, R., et al. (2014) · Journal of Medicinal Chemistry · doi:10.1021/jm4004285 · Cited by 2,164
Rational design of potent sialidase-based inhibitors of influenza virus replication
von Itzstein, M., Wu, W.-Y., Kok, G. B., Pegg, M. S., Dyason, J. C., Jin, B., Van Phan, T., Smythe, M. L., White, H. F., Oliver, S. W., et al. (1993) · Nature · doi:10.1038/363418a0 · Cited by 1,862
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Pagadala, N. S., Syed, K., & Tuszynski, J. (2017) · Biophysical Reviews · doi:10.1007/s12551-016-0247-1 · Cited by 1,522
Metadata
- Authors
- Goodford, P. J.
- Venue
- Journal of Medicinal Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 1985-07
- Volume
- 28
- Issue
- 7
- Pages
- 849-857
- ISSN
- 0022-2623 (ISSN-L)
- 1520-4804
- OpenAlex
- W2080653934
- Cited by
- 2,634
- References
- 0
- FWCI
- 10.55
- Type
- journal article
- Language
- en
- Open access
- closed
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- Goodford, P. J. (1985). A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. Journal of Medicinal Chemistry. https://doi.org/10.1021/jm00145a002
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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