Time-lagged t-distributed stochastic neighbor embedding (t-SNE) of molecular simulation trajectories

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60461373%3A22330%2F20%3A43920852" target="_blank" >RIV/60461373:22330/20:43920852 - isvavai.cz</a>
Alternative codes found
RIV/60461373:22340/20:43920852
Result on the web
<a href="https://www.frontiersin.org/articles/10.3389/fmolb.2020.00132/full" target="_blank" >https://www.frontiersin.org/articles/10.3389/fmolb.2020.00132/full</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.3389/fmolb.2020.00132" target="_blank" >10.3389/fmolb.2020.00132</a>

Result language
angličtina
Original language name
Time-lagged t-distributed stochastic neighbor embedding (t-SNE) of molecular simulation trajectories
Original language description
Molecular simulation trajectories represent high-dimensional data. Such data can be visualized by methods of dimensionality reduction. Non-linear dimensionality reduction methods are likely to be more efficient than linear ones due to the fact that motions of atoms are non-linear. Here we test a popular non-linear t-distributed Stochastic Neighbor Embedding (t-SNE) method on analysis of trajectories of 200 ns alanine dipeptide dynamics and 208 μs Trp-cage folding and unfolding. Furthermore, we introduce a time-lagged variant of t-SNE in order to focus on rarely occurring transitions in the molecular system. This time-lagged t-SNE efficiently separates states according to distance in time. Using this method it is possible to visualize key states of studied systems (e.g., unfolded and folded protein) as well as possible kinetic traps using a two-dimensional plot. Time-lagged t-SNE is a visualization method and other applications, such as clustering and free energy modeling, must be done with caution.
Czech name
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Czech description
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Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10602 - Biology (theoretical, mathematical, thermal, cryobiology, biological rhythm), Evolutionary biology

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
2020
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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