The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
A Bias-Exchange Approach to Protein Folding
Open accessAbstract
By suitably extending a recent approach [Bussi, G.; et al. J. Am. Chem. Soc. 2006, 128, 13435] we introduce a powerful methodology that allows the parallel reconstruction of the free energy of a system in a virtually unlimited number of variables. Multiple metadynamics simulations of the same system at the same temperature are performed, biasing each replica with a time-dependent potential constructed in a different set of collective variables. Exchanges between the bias potentials in the different variables are periodically allowed according to a replica exchange scheme. Due to the efficaciously multidimensional nature of the bias the method allows exploring complex free energy landscapes with high efficiency. The usefulness of the method is demonstrated by performing an atomistic simulation in explicit solvent of the folding of a Triptophane cage miniprotein. It is shown that the folding free energy landscape can be fully characterized starting from an extended conformation with use of only 40 ns of simulation on 8 replicas.
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Cites
Laio, A., & Parrinello, M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202427399 · Cited by 5,626
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Neidigh, J. W., Fesinmeyer, R. M., & Andersen, N. H. (2002) · Nature Structural Biology · doi:10.1038/nsb798 · Cited by 793
Assessing 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
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Laio, A., & Gervasio, F. L. (2008) · Reports on Progress in Physics · doi:10.1088/0034-4885/71/12/126601 · Cited by 1,619
Self-citationUsing collective variables to drive molecular dynamics simulations
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Invernizzi, M., & Parrinello, M. (2020) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.0c00497 · Cited by 359
i-PI 2.0: A universal force engine for advanced molecular simulations
Kapil, V., Rossi, M., Marsalek, O., Petraglia, R., Litman, Y., Spura, T., Cheng, B., Cuzzocrea, A., Meißner, R. H., Wilkins, D. M., et al. (2019) · Computer Physics Communications · doi:10.1016/j.cpc.2018.09.020 · Cited by 357
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Piana, S., Laio, A., Marinelli, F., Van Troys, M., Bourry, D., Ampe, C., & Martins, J. C. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.10.020 · Cited by 48
Self-citationToward the Prediction of Binding Events in Very Flexible, Allosteric, Multidomain Proteins
Basciu, A., Athar, M., Kurt, H., Neville, C., Malloci, G., Muredda, F. C., Bosin, A., Ruggerone, P., Bonvin, A. M. J. J., & Vargiu, A. V. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.4c01810 · Cited by 12
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Metadata
- Authors
- Piana, S., & Laio, A.
- Venue
- The Journal of Physical Chemistry B
- Publisher
- American Chemical Society (ACS)
- Published
- 2007-04-10
- Volume
- 111
- Issue
- 17
- Pages
- 4553-4559
- ISSN
- 1520-5207 (ISSN-L)
- 1520-6106
- OpenAlex
- W1995907662
- Cited by
- 598
- References
- 3
- FWCI
- 6.11
- Type
- journal article
- Language
- en
- Open access
- green
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