The DOI matches its Crossref record; 80 of the 80 references it cites were found in a registry or an index.
Balancing Solvation and Intramolecular Interactions: Toward a Consistent Generalized Born Force Field
Open accessAbstract
The efficient and accurate characterization of solvent effects is a key element in the theoretical and computational study of biological problems. Implicit solvent models, particularly generalized Born (GB) continuum electrostatics, have emerged as an attractive tool to study the structure and dynamics of biomolecules in various environments. Despite recent advances in this methodology, there remain limitations in the parametrization of many of these models. In the present work, we demonstrate that it is possible to achieve a balanced implicit solvent force field by further optimizing the input atomic radii in combination with adjusting the protein backbone torsional energetics. This parameter optimization is guided by the potentials of mean force (PMFs) between amino acid polar groups, calculated from explicit solvent free energy simulations, and by conformational equilibria of short peptides, obtained from extensive folding and unfolding replica exchange molecular dynamics (REX-MD) simulations. Through the application of this protocol, the delicate balance between the competing solvation forces and intramolecular forces appears to be better captured, and correct conformational equilibria for a range of both helical and beta-hairpin peptides are obtained. The same optimized force field also successfully folds both beta-hairpin trpzip2 and mini-protein Trp-Cage, indicating that it is quite robust. Such a balanced, physics-based force field will be highly applicable to a range of biological problems including protein folding and protein structural dynamics.
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Ryckaert, J.-P., Ciccotti, G., & Berendsen, H. J. C. (1977) · Journal of Computational Physics · doi:10.1016/0021-9991(77)90098-5 · Cited by 21,239
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., & Karplus, M. (1983) · Journal of Computational Chemistry · doi:10.1002/jcc.540040211 · Cited by 14,944
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., et al. (1998) · The Journal of Physical Chemistry B · doi:10.1021/jp973084f · Cited by 14,311
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
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
Torrie, G. M., & Valleau, J. P. (1977) · Journal of Computational Physics · doi:10.1016/0021-9991(77)90121-8 · Cited by 6,091
Replica-exchange molecular dynamics method for protein folding
Sugita, Y., & Okamoto, Y. (1999) · Chemical Physics Letters · doi:10.1016/s0009-2614(99)01123-9 · Cited by 4,514
Semianalytical treatment of solvation for molecular mechanics and dynamics
Still, W. C., Tempczyk, A., Hawley, R. C., & Hendrickson, T. (1990) · Journal of the American Chemical Society · doi:10.1021/ja00172a038 · Cited by 3,643
Mackerell, A. D., Feig, M., & Brooks, C. L. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20065 · Cited by 3,319
Self-citationClassical Electrostatics in Biology and Chemistry
Honig, B., & Nicholls, A. (1995) · Science · doi:10.1126/science.7761829 · Cited by 2,879
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
Cited by
CHARMM: The biomolecular simulation program
Brooks, B. R., Brooks, C. L., Mackerell, A. D., Nilsson, L., Petrella, R. J., Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch, S., et al. (2009) · Journal of Computational Chemistry · doi:10.1002/jcc.21287 · Cited by 8,939
Self-citationGeneralized Born Implicit Solvent Models for Biomolecules
Onufriev, A. V., & Case, D. A. (2019) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-052118-115325 · Cited by 286
Biomolecular simulation and modelling: status, progress and prospects
van der Kamp, M. W., Shaw, K. E., Woods, C. J., & Mulholland, A. J. (2008) · Journal of The Royal Society Interface · doi:10.1098/rsif.2008.0105.focus · Cited by 90
Critical Importance of Length-Scale Dependence in Implicit Modeling of Hydrophobic Interactions
Chen, J., & Brooks, C. L. (2007) · Journal of the American Chemical Society · doi:10.1021/ja068383+ · Cited by 47
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Metadata
- Authors
- Chen, J., Im, W., & Brooks, C. L.
- Venue
- Journal of the American Chemical Society
- Publisher
- American Chemical Society (ACS)
- Published
- 2006-03-01
- Volume
- 128
- Issue
- 11
- Pages
- 3728-3736
- ISSN
- 0002-7863 (ISSN-L)
- 1520-5126
- OpenAlex
- W2007965478
- Cited by
- 338
- References
- 80
- FWCI
- 9.45
- Type
- journal article
- Language
- en
- Open access
- green
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