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Solvation Free Energy of Biomacromolecules: Parameters for a Modified Generalized Born Model Consistent with the AMBER Force Field
Abstract
The generalized Born (GB) model provides rapid estimates of the electrostatic free energies of solvation for diverse molecules and molecular ions. This method is expected to be of considerable utility for studies of solvation in macromolecular and biological systems. Calculations on biological molecules are typically based on empirical energy functions, each of which have their own prescriptions for determining net atomic charges. For maximum compatibility, GB parameters tailored to specific force fields are required. The development of parameters compatible with the AMBER force field is described. The method is used to estimate free energies of A and B form structures of DNA obtained from molecular dynamics simulations. The results provide an account of the conformational preferences of right-handed DNA in solution.
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Citations
Cited by
Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics
Cramer, C. J., & Truhlar, D. G. (1999) · Chemical Reviews · doi:10.1021/cr960149m · Cited by 2,308
An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0
Malde, A. K., Zuo, L., Breeze, M., Stroet, M., Poger, D., Nair, P. C., Oostenbrink, C., & Mark, A. E. (2011) · Journal of Chemical Theory and Computation · doi:10.1021/ct200196m · Cited by 1,872
Massova, I., & Kollman, P. A. (2000) · Perspectives in Drug Discovery and Design · doi:10.1023/a:1008763014207 · Cited by 1,015
Theoretical Methods for the Description of the Solvent Effect in Biomolecular Systems
Orozco, M., & Luque, F. J. (2000) · Chemical Reviews · doi:10.1021/cr990052a · Cited by 622
An improved protein decoy set for testing energy functions for protein structure prediction
Tsai, J., Bonneau, R., Morozov, A. V., Kuhlman, B., Rohl, C. A., & Baker, D. (2003) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10454 · Cited by 158
Li, W. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg149 · Cited by 31
Metadata
- Authors
- Jayaram, B., Sprous, D., & Beveridge, D. L.
- Venue
- The Journal of Physical Chemistry B
- Publisher
- American Chemical Society (ACS)
- Published
- 1998-11-01
- Volume
- 102
- Issue
- 47
- Pages
- 9571-9576
- ISSN
- 1520-5207 (ISSN-L)
- 1520-6106
- OpenAlex
- W2098362016
- Cited by
- 258
- References
- 0
- FWCI
- 3.49
- Type
- journal article
- Language
- en
- Open access
- closed
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