The DOI matches its Crossref record.
A temperature predictor for parallel tempering simulations
Abstract
An algorithm is proposed that generates a set of temperatures for use in parallel tempering simulations (also known as temperature-replica exchange molecular dynamics simulations) of proteins to obtain a desired exchange probability Pdes. The input consists of the number of protein atoms and water molecules in the system, information about the use of constraints and virtual sites and the lower temperature limits. The temperatures generated yield probabilities which are very close to Pdes (correlation 97%), independent of force field and over a wide temperature range. To facilitate its use, the algorithm has been implemented as a web server at .
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
Cited by
Ou, X., Xue, B., Lao, Y., Wutthinitikornkit, Y., Tian, R., Zou, A., Yang, L., Wang, W., Cao, Y., & Li, J. (2020) · Science Advances · doi:10.1126/sciadv.abb7620 · Cited by 109
Biomolecular simulation and modelling: status, progress and prospects
van der Kamp, M. W., Shaw, K. E., Woods, C. J., & Mulholland, A. J. (2008) · Journal of The Royal Society Interface · doi:10.1098/rsif.2008.0105.focus · Cited by 90
Kinetic pathways of water exchange in the first hydration shell of magnesium
Schwierz, N. (2020) · The Journal of Chemical Physics · doi:10.1063/1.5144258 · Cited by 52
Development of second generation peptides modulating cellular adiponectin receptor responses
Otvos, L., Knappe, D., Hoffmann, R., Kovalszky, I., Olah, J., Hewitson, T. D., Stawikowska, R., Stawikowski, M., Cudic, P., Lin, F., et al. (2014) · Frontiers in Chemistry · doi:10.3389/fchem.2014.00093 · Cited by 50
Brown, A. H., Rodger, P. M., Evans, J. S., & Walsh, T. R. (2014) · Biomacromolecules · doi:10.1021/bm501263s · Cited by 28
Metadata
- Authors
- Patriksson, A., & van der Spoel, D.
- Venue
- Physical Chemistry Chemical Physics
- Publisher
- Royal Society of Chemistry (RSC)
- Published
- 2008
- Volume
- 10
- Issue
- 15
- Pages
- 2073
- ISSN
- 1463-9076 (ISSN-L)
- 1463-9084
- OpenAlex
- W2032363535
- Cited by
- 492
- References
- 0
- FWCI
- 4.71
- Type
- journal article
- Language
- en
- Open access
- closed
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: A temperature predictor for parallel tempering simulations. https://app.cochat.ai/papers/10.1039/b716554d
- The paper
- Patriksson, A., & van der Spoel, D. (2008). A temperature predictor for parallel tempering simulations. Physical Chemistry Chemical Physics. https://doi.org/10.1039/b716554d
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.
