The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Long‐Time Protein Folding Dynamics from Short‐Time Molecular Dynamics Simulations
Open accessAbstract
Protein folding involves physical timescales—microseconds to seconds—that are too long to be studied directly by straightforward molecular dynamics simulation, where the fundamental timestep is constrained to femtoseconds. Here we show how the long‐time statistical dynamics of a simple solvated biomolecular system can be well described by a discrete‐state Markov chain model constructed from trajectories that are an order of magnitude shorter than the longest relaxation times of the system. This suggests that such models, appropriately constructed from short molecular dynamics simulations, may have utility in the study of long‐time conformational dynamics.
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Citations
Cites
Principles that Govern the Folding of Protein Chains
Anfinsen, C. B. (1973) · Science · doi:10.1126/science.181.4096.223 · Cited by 7,096
Reaction coordinates of biomolecular isomerization
Bolhuis, P. G., Dellago, C., & Chandler, D. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.100127697 · Cited by 426
Automatic Method for Identifying Reaction Coordinates in Complex Systems
Ma, A., & Dinner, A. R. (2005) · The Journal of Physical Chemistry B · doi:10.1021/jp045546c · Cited by 400 · cited 1×
“The slow degrees of freedom for terminally blocked alanine peptide (neglecting those involving solvent motion) can be captured by the two backbone torsion angles labeled φ and ψ (see Figure 1) [5, 29].”
Background
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
Self-citationPyEMMA 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
Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations
Noé, F., Schütte, C., Vanden-Eijnden, E., Reich, L., & Weikl, T. R. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0905466106 · Cited by 820
Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1−39)
Voelz, V. A., Bowman, G. R., Beauchamp, K., & Pande, V. S. (2010) · Journal of the American Chemical Society · doi:10.1021/ja9090353 · Cited by 503
Transition networks for modeling the kinetics of conformational change in macromolecules
Noé, F., & Fischer, S. (2008) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2008.01.008 · Cited by 481
Metadata
- Authors
- Chodera, J. D., Swope, W. C., Pitera, J. W., & Dill, K. A.
- Venue
- Multiscale Modeling & Simulation
- Published
- 2006-01
- Volume
- 5
- Issue
- 4
- Pages
- 1214-1226
- ISSN
- 1540-3459 (ISSN-L)
- 1540-3467
- OpenAlex
- W2044201287
- Cited by
- 220
- References
- 3
- FWCI
- 4.30
- Type
- journal article
- Language
- en
- Open access
- green
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- Chodera, J. D., Swope, W. C., Pitera, J. W., & Dill, K. A. (2006). Long‐Time Protein Folding Dynamics from Short‐Time Molecular Dynamics Simulations. Multiscale Modeling & Simulation. https://doi.org/10.1137/06065146x
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