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Microsecond timescale MD simulations at the transition state of Pm HMGR predict remote allosteric residues
Open accessPublished version of a preprint
Abstract
Transition state force fields enable MD simulations at the transition state of HMGCoA reductase that sample the transition state ensemble on the μs timescale to identify remote residues that affect the reaction rate.
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Markov state models of biomolecular conformational dynamics
Chodera, J. D., & Noé, F. (2014) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2014.04.002 · Cited by 776
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Metadata
- Authors
- Quinn, T. R., Steussy, C. N., Haines, B. E., Lei, J., Wang, W., Sheong, F. K., Stauffacher, C. V., Huang, X., Norrby, P.-O., Helquist, P., & Wiest, O.
- Affiliations
- University of Notre Dame (US)
- Purdue University West Lafayette (US)
- Westmont College (US)
- Sun Yat-sen University (CN)
- Hong Kong University of Science and Technology (HK)
- Corresponding author
- Wiest, Olaf
- ORCID
- Venue
- Chemical Science
- Publisher
- Royal Society of Chemistry (RSC)
- Published
- 2021
- Volume
- 12
- Issue
- 18
- Pages
- 6413-6418
- ISSN
- 2041-6520 (ISSN-L)
- 2041-6539
- PMC
- PMC8115266
- OpenAlex
- W3142343720
- Cited by
- 12
- References
- 1
- Citations by year
- 2025: 4 · 2024: 1 · 2023: 3 · 2022: 1 · 2021: 2
- FWCI
- 0.55
- Type
- journal article
- Language
- en
- Open access
- diamond
- doi.org
- Licence
- Locations
- Chemical Science (publishedVersion, cc-by-nc)
- ChemRxiv (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Royal College of Surgeons in Ireland (submittedVersion, cc-by-nc-nd)
- Rare & Special e-Zone (The Hong Kong University of Science and Technology) (submittedVersion)
- Funders
- National Institute of General Medical Sciences (T32GM075762, 1R01GM111645)
- Research Grants Council, University Grants Committee (AoE/P-705/16)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Organic Chemistry › Physical Organic Chemistry and Reaction Kinetics
- Physical Sciences › Chemistry › Inorganic Chemistry › Metal-Catalyzed Oxygenation Mechanisms
- Keywords
- hydroxymethylbilane synthase, transition state, allosteric site prediction, site-directed mutagenesis
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.
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