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Efficient numerical reconstruction of protein folding kinetics with partial path sampling and pathlike variables.

Juraszek, J; Saladino, G; van Erp, TS; Gervasio, FL; (2013) Efficient numerical reconstruction of protein folding kinetics with partial path sampling and pathlike variables. Phys Rev Lett , 110 (10) , Article 108106. 10.1103/PhysRevLett.110.108106. Green open access

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Abstract

Numerically predicting rate constants of protein folding and other relevant biological events is still a significant challenge. We show that the combination of partial path transition interface sampling with the optimal interfaces and free-energy profiles provided by path collective variables makes the rate calculation for practical biological applications feasible and efficient. This methodology can reproduce the experimental rate constant of Trp-cage miniprotein folding with the same level of accuracy as transition path sampling at a fraction of the cost.

Type: Article
Title: Efficient numerical reconstruction of protein folding kinetics with partial path sampling and pathlike variables.
Location: United States
Open access status: An open access version is available from UCL Discovery
DOI: 10.1103/PhysRevLett.110.108106
Publisher version: http://dx.doi.org/10.1103/PhysRevLett.110.108106
Language: English
Additional information: © 2013 American Physical Society
Keywords: Hydrophobic and Hydrophilic Interactions, Kinetics, Models, Chemical, Models, Molecular, Peptides, Protein Folding, Protein Structure, Secondary, Thermodynamics
UCL classification: UCL
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences > Dept of Chemistry
URI: https://discovery.ucl.ac.uk/id/eprint/1389039
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