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A rapid finite difference algorithm, utilizing successive over‐relaxation to solve the Poisson–Boltzmann equation
Abstract
An efficient algorithm is presented for the numerical solution of the Poisson–Boltzmann equation by the finite difference method of successive over‐relaxation. Improvements include the rapid estimation of the optimum relaxation parameter, reduction in number of operations per iteration, and vector‐oriented array mapping. The algorithm has been incorporated into the electrostatic program DelPhi, reducing the required computing time by between one and two orders of magnitude. As a result the estimation of electrostatic effects such as solvent screening, ion distributions, and solvation energies of small solutes and biological macromolecules in solution, can be performed rapidly, and with minimal computing facilities.
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Database resources of the national center for biotechnology information
Sayers, E. W., Bolton, E. E., Brister, J. R., Canese, K., Chan, J., Comeau, D. C., Connor, R., Funk, K., Kelly, C., Kim, S., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1112 · Cited by 2,812
Onufriev, A., Bashford, D., & Case, D. A. (2004) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.20033 · Cited by 2,507
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
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
Massova, I., & Kollman, P. A. (2000) · Perspectives in Drug Discovery and Design · doi:10.1023/a:1008763014207 · Cited by 1,015
Metadata
- Authors
- Nicholls, A., & Honig, B.
- Venue
- Journal of Computational Chemistry
- Publisher
- Wiley
- Published
- 1991-05
- Volume
- 12
- Issue
- 4
- Pages
- 435-445
- ISSN
- 0192-8651 (ISSN-L)
- 1096-987X
- OpenAlex
- W2127116852
- Cited by
- 1,263
- References
- 0
- FWCI
- 17.01
- Type
- journal article
- Language
- en
- Open access
- closed
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- Nicholls, A., & Honig, B. (1991). A rapid finite difference algorithm, utilizing successive over‐relaxation to solve the Poisson–Boltzmann equation. Journal of Computational Chemistry. https://doi.org/10.1002/jcc.540120405
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