The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Using path sampling to build better Markovian state models: Predicting the folding rate and mechanism of a tryptophan zipper beta hairpin
Abstract
We propose an efficient method for the prediction of protein folding rate constants and mechanisms. We use molecular dynamics simulation data to build Markovian state models (MSMs), discrete representations of the pathways sampled. Using these MSMs, we can quickly calculate the folding probability (Pfold) and mean first passage time of all the sampled points. In addition, we provide techniques for evaluating these values under perturbed conditions without expensive recomputations. To demonstrate this method on a challenging system, we apply these techniques to a two-dimensional model energy landscape and the folding of a tryptophan zipper beta hairpin.
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Equation of State Calculations by Fast Computing Machines
Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H., & Teller, E. (1953) · The Journal of Chemical Physics · doi:10.1063/1.1699114 · Cited by 37,192
Golub, G. (2012) · doi:10.56021/9781421407944 · Cited by 34,505
Computer Simulation of Liquids
Allen, M. P., & Tildesley, D. J. (2017) · doi:10.1093/oso/9780198803195.001.0001 · Cited by 20,945
Shea, J.-E., & Brooks III, C. L. (2001) · Annual Review of Physical Chemistry · doi:10.1146/annurev.physchem.52.1.499 · Cited by 481
Cited by
Markov models of molecular kinetics: Generation and validation
Prinz, J.-H., Wu, H., Sarich, M., Keller, B., Senne, M., Held, M., Chodera, J. D., Schütte, C., & Noé, F. (2011) · The Journal of Chemical Physics · doi:10.1063/1.3565032 · Cited by 1,275
Dill, K. A., Ozkan, S. B., Shell, M. S., & Weikl, T. R. (2008) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.37.092707.153558 · Cited by 1,163
PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models
Scherer, M. K., Trendelkamp-Schroer, B., Paul, F., Pérez-Hernández, G., Hoffmann, M., Plattner, N., Wehmeyer, C., Prinz, J.-H., & Noé, F. (2015) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5b00743 · Cited by 1,163
Everything you wanted to know about Markov State Models but were afraid to ask
Pande, V. S., Beauchamp, K., & Bowman, G. R. (2010) · Methods · doi:10.1016/j.ymeth.2010.06.002 · Cited by 698
Self-citationComplete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
Buch, I., Giorgino, T., & De Fabritiis, G. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1103547108 · Cited by 655
Metadata
- Authors
- Singhal, N., Snow, C. D., & Pande, V. S.
- Venue
- The Journal of Chemical Physics
- Publisher
- AIP Publishing
- Published
- 2004-07-01
- Volume
- 121
- Issue
- 1
- Pages
- 415-425
- ISSN
- 0021-9606 (ISSN-L)
- 1089-7690
- OpenAlex
- W1977969550
- Cited by
- 269
- References
- 4
- FWCI
- 5.25
- Type
- journal article
- Language
- en
- Open access
- closed
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- Singhal, N., Snow, C. D., & Pande, V. S. (2004). Using path sampling to build better Markovian state models: Predicting the folding rate and mechanism of a tryptophan zipper beta hairpin. The Journal of Chemical Physics. https://doi.org/10.1063/1.1738647
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