The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Free-Energy Landscape for β Hairpin Folding from Combined Parallel Tempering and Metadynamics
Abstract
We develop a new free-energy method, based on the combination of parallel tempering and metadynamics, and apply this method to the calculation of the free-energy landscape of the folding beta hairpin in explicit water. We show that the combined method greatly improves the performance of both parallel tempering and metadynamics. In particular, we are able to sample the high free-energy regions, which are not accessible with conventional parallel tempering. We use our results to calculate the difference in entropy and enthalpy between the folded and the unfolded state and to characterize the most populated configurations in the relevant free-energy basins.
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Cites
VMD: visual molecular dynamics
Humphrey, W., Dalke, A., & Schulten, K. (1996) · Journal of Molecular Graphics · doi:10.1016/0263-7855(96)00018-5 · Cited by 66,952
Laio, A., & Parrinello, M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202427399 · Cited by 5,626
Self-citationAssessing the Accuracy of Metadynamics
Laio, A., Rodriguez-Fortea, A., Gervasio, F. L., Ceccarelli, M., & Parrinello, M. (2005) · The Journal of Physical Chemistry B · doi:10.1021/jp045424k · Cited by 517
Self-citationFolding funnels and energy landscapes of larger proteins within the capillarity approximation
Wolynes, P. G. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.12.6170 · Cited by 218
Cited by
Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
Barducci, A., Bussi, G., & Parrinello, M. (2008) · Physical Review Letters · doi:10.1103/physrevlett.100.020603 · Cited by 3,184
Self-citationPLUMED: A portable plugin for free-energy calculations with molecular dynamics
Bonomi, M., Branduardi, D., Bussi, G., Camilloni, C., Provasi, D., Raiteri, P., Donadio, D., Marinelli, F., Pietrucci, F., Broglia, R. A., et al. (2009) · Computer Physics Communications · doi:10.1016/j.cpc.2009.05.011 · Cited by 1,875
Self-citationLaio, A., & Gervasio, F. L. (2008) · Reports on Progress in Physics · doi:10.1088/0034-4885/71/12/126601 · Cited by 1,619
Self-citationRole of Molecular Dynamics and Related Methods in Drug Discovery
De Vivo, M., Masetti, M., Bottegoni, G., & Cavalli, A. (2016) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.5b01684 · Cited by 1,297
Using collective variables to drive molecular dynamics simulations
Fiorin, G., Klein, M. L., & Hénin, J. (2013) · Molecular Physics · doi:10.1080/00268976.2013.813594 · Cited by 1,053
Metadata
- Authors
- Bussi, G., Gervasio, F. L., Laio, A., & Parrinello, M.
- Venue
- Journal of the American Chemical Society
- Publisher
- American Chemical Society (ACS)
- Published
- 2006-09-21
- Volume
- 128
- Issue
- 41
- Pages
- 13435-13441
- ISSN
- 0002-7863 (ISSN-L)
- 1520-5126
- OpenAlex
- W1991329443
- Cited by
- 505
- References
- 4
- FWCI
- 4.54
- Type
- journal article
- Language
- en
- Open access
- closed
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