Nonlinear vs. linear biasing in Trp-cage folding simulations

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60461373%3A22330%2F15%3A43899754" target="_blank" >RIV/60461373:22330/15:43899754 - isvavai.cz</a>
Alternative codes found
RIV/00216224:14610/15:00080979
Result on the web
<a href="http://scitation.aip.org/content/aip/journal/jcp/142/11/10.1063/1.4914828" target="_blank" >http://scitation.aip.org/content/aip/journal/jcp/142/11/10.1063/1.4914828</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1063/1.4914828" target="_blank" >10.1063/1.4914828</a>

Result language
angličtina
Original language name
Nonlinear vs. linear biasing in Trp-cage folding simulations
Original language description
Biased simulations have great potential for the study of slow processes, including protein folding. Atomic motions in molecules are nonlinear, which suggests that simulations with enhanced sampling of collective motions traced by nonlinear dimensionalityreduction methods may perform better than linear ones. In this study, we compare an unbiased folding simulation of the Trp-cage miniprotein with metadynamics simulations using both linear (principle component analysis) and nonlinear (Isomap) low dimensional embeddings as collective variables. Folding of the mini-protein was successfully simulated in 200 ns simulation with linear biasing and non-linear motion biasing. The folded state was correctly predicted as the free energy minimum in both simulations. We found that the advantage of linear motion biasing is that it can sample a larger conformational space, whereas the advantage of nonlinear motion biasing lies in slightly better resolution of the resulting free energy surface. In ter
Czech name
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Czech description
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Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
CE - Biochemistry
OECD FORD branch
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Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year
2015
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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