Why are MD simulated protein folding times wrong?

Nerukh, Dmitry (2010). Why are MD simulated protein folding times wrong? IN: Advances in Computational Biology. Arabnia, Hamid R. (ed.) Advances in Experimental Medicine and Biology, Part 3 . Springer.

Abstract

The question of significant deviations of protein folding times simulated using molecular dynamics from experimental values is investigated. It is shown that in the framework of Markov State Model (MSM) describing the conformational dynamics of peptides and proteins, the folding time is very sensitive to the simulation model parameters, such as forcefield and temperature. Using two peptides as examples, we show that the deviations in the folding times can reach an order of magnitude for modest variations of the molecular model. We, therefore, conclude that the folding rate values obtained in molecular dynamics simulations have to be treated with care.

Publication DOI: https://doi.org/10.1007/978-1-4419-5913-3_36
Divisions: Engineering & Applied Sciences > Mathematics
Engineering & Applied Sciences > Systems analytics research institute (SARI)
Additional Information: The original publication is available at www.springerlink.com
Uncontrolled Keywords: molecular dynamics,MSM,protein folding,simulation models,VPAL,Biochemistry, Genetics and Molecular Biology(all),Medicine(all)
Full Text Link: http://www.springer.com/life+sciences/bioinformatics/book/978-1-4419-5912-6
Related URLs: http://www.scopus.com/inward/record.url?scp=79952198807&partnerID=8YFLogxK (Scopus URL)
Published Date: 2010-10-06
Authors: Nerukh, Dmitry ( 0000-0001-9005-9919)

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