The DOI matches its Crossref record; 42 of the 42 references it cites were found in a registry or an index.
Reaction coordinates and rates from transition paths
Open accessAbstract
The molecular mechanism of a reaction in solution is reflected in its transition-state ensemble and transition paths. We use a Bayesian formula relating the equilibrium and transition-path ensembles to identify transition states, rank reaction coordinates, and estimate rate coefficients. We also introduce a variational procedure to optimize reaction coordinates. The theory is illustrated with applications to protein folding and the dipole reorientation of an ordered water chain inside a carbon nanotube. To describe the folding of a simple model of a three-helix bundle protein, we variationally optimize the weights of a projection onto the matrix of native and nonnative amino acid contacts. The resulting one-dimensional reaction coordinate captures the folding transition state, with formation and packing of helix 2 and 3 constituting the bottleneck for folding.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Comparison of simple potential functions for simulating liquid water
Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983) · The Journal of Chemical Physics · doi:10.1063/1.445869 · Cited by 41,298
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
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., & Kollman, P. A. (1995) · Journal of the American Chemical Society · doi:10.1021/ja00124a002 · Cited by 13,103
Reaction-rate theory: fifty years after Kramers
Hänggi, P., Talkner, P., & Borkovec, M. (1990) · Reviews of Modern Physics · doi:10.1103/revmodphys.62.251 · Cited by 6,154
Dynamic Light Scattering: Applications of Photon Correlation Spectroscopy
(1985) · Springer eBooks · doi:10.1007/978-1-4613-2389-1 · Cited by 4,856
Water conduction through the hydrophobic channel of a carbon nanotube
Hummer, G., Rasaiah, J. C., & Noworyta, J. P. (2001) · Nature · doi:10.1038/35102535 · Cited by 3,557
Self-citationNonequilibrium Statistical Mechanics
Zwanzig, R. (2001) · doi:10.1093/oso/9780195140187.001.0001 · Cited by 2,051
T RANSITION P ATH S AMPLING : Throwing Ropes Over Rough Mountain Passes, in the Dark
Bolhuis, P. G., Chandler, D., Dellago, C., & Geissler, P. L. (2002) · Annual Review of Physical Chemistry · doi:10.1146/annurev.physchem.53.082301.113146 · Cited by 1,972
Onsager, L. (1938) · Physical Review · doi:10.1103/physrev.54.554 · Cited by 1,887
Statistical mechanics of isomerization dynamics in liquids and the transition state approximation
Chandler, D. (1978) · The Journal of Chemical Physics · doi:10.1063/1.436049 · Cited by 1,415
Cited by
Computer Simulation of Liquids
Allen, M. P., & Tildesley, D. J. (2017) · doi:10.1093/oso/9780198803195.001.0001 · Cited by 20,945
How fast-folding proteins fold
Lindorff-Larsen, K., Piana, S., Dror, R. O., & Shaw, D. E. (2011) · Science · doi:10.1126/science.1208351 · Cited by 1,980
Atomic-level characterization of the structural dynamics of proteins
Shaw, D. E., Maragakis, P., Lindorff-Larsen, K., Piana, S., Dror, R. O., Eastwood, M. P., Bank, J. A., Jumper, J. M., Salmon, J. K., Shan, Y., et al. (2010) · Science · doi:10.1126/science.1187409 · Cited by 1,923
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
Native contacts determine protein folding mechanisms in atomistic simulations
Best, R. B., Hummer, G., & Eaton, W. A. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1311599110 · Cited by 594
Self-citation
Metadata
- Authors
- Best, R. B., & Hummer, G.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2005-04-06
- Volume
- 102
- Issue
- 19
- Pages
- 6732-6737
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2145326890
- Cited by
- 511
- References
- 42
- FWCI
- 5.30
- Type
- journal article
- Language
- en
- Open access
- green
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Reaction coordinates and rates from transition paths. https://app.cochat.ai/papers/10.1073/pnas.0408098102
- The paper
- Best, R. B., & Hummer, G. (2005). Reaction coordinates and rates from transition paths. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.0408098102
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
