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 |
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Divisions: | College of Engineering & Physical 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,General Biochemistry,Genetics and Molecular Biology,General Medicine |
ISBN: | 9781441959126 |
Last Modified: | 30 Sep 2024 09:00 |
Date Deposited: | 01 Nov 2010 13:18 |
Full Text Link: |
http://www.spri ... 8-1-4419-5912-6 |
Related URLs: |
http://www.scop ... tnerID=8YFLogxK
(Scopus URL) |
PURE Output Type: | Chapter |
Published Date: | 2010-10-06 |
Authors: |
Nerukh, Dmitry
(
0000-0001-9005-9919)
|