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Free Energy Calculations by Computer Simulation
Abstract
A fundamental problem in chemistry and biochemistry is understanding the role of solvation in determining molecular properties. Recent advances in statistical mechanical theory and molecular dynamics methodology can be used to solve this problem with the aid of supercomputers. By using these advances the free energies of solvation of all the chemical classes of amino acid side chains, four nucleic acid bases and other organic molecules can be calculated. The effect of a site-specific mutation on the stability of trypsin is predicted. The results are in good agreement with available experiments.
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Cited by
THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method
Kumar, S., Rosenberg, J. M., Bouzida, D., Swendsen, R. H., & Kollman, P. A. (1992) · Journal of Computational Chemistry · doi:10.1002/jcc.540130812 · Cited by 6,808
Self-citationDuan, Y., Wu, C., Chowdhury, S., Lee, M. C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T., et al. (2003) · Journal of Computational Chemistry · doi:10.1002/jcc.10349 · Cited by 4,441
Self-citationPearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., DeBolt, S., Ferguson, D., Seibel, G., & Kollman, P. (1995) · Computer Physics Communications · doi:10.1016/0010-4655(95)00041-d · Cited by 3,124
Self-citationForesman, J. B., Keith, T. A., Wiberg, K. B., Snoonian, J., & Frisch, M. J. (1996) · The Journal of Physical Chemistry · doi:10.1021/jp960488j · Cited by 1,257
Prediction of protein stability changes for single‐site mutations using support vector machines
Cheng, J., Randall, A., & Baldi, P. (2006) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.20810 · Cited by 1,160
Metadata
- Authors
- Bash, P. A., Singh, U. C., Langridge, R., & Kollman, P. A.
- Venue
- Science
- Published
- 1987-05
- Volume
- 236
- Issue
- 4801
- Pages
- 564-568
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2083624153
- Cited by
- 413
- References
- 0
- FWCI
- 7.40
- Type
- journal article
- Language
- en
- Open access
- closed
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- Bash, P. A., Singh, U. C., Langridge, R., & Kollman, P. A. (1987). Free Energy Calculations by Computer Simulation. Science. https://doi.org/10.1126/science.3576184
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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.
