High-resolution visualisation of the states and pathways sampled in molecular dynamics simulations

TitleHigh-resolution visualisation of the states and pathways sampled in molecular dynamics simulations
Publication TypeJournal Article
Year of Publication2014
AuthorsBlöchliger N., Vitalis A., Caflisch A.
JournalScientific Reports
Volume4
Pagination6264
Date PublishedAug 2014
Type of ArticleResearch Article
ISSN2045-2322
Keywordsdata analysis, data visualization, free energy landscape, metastable states, molecular dynamics, pathways, Protein Folding, scalable algorithms
Abstract

We have recently developed a scalable algorithm for ordering the instantaneous observations of a dynamical system evolving continuously in time. Here, we apply the method to long molecular dynamics trajectories. The procedure requires only a pairwise, geometrical distance as input. Suitable annotations of both structural and kinetic nature reveal the free energy basins visited by biomolecules. The profile is supplemented by a trace of the temporal evolution of the system highlighting the sequence of events. We demonstrate that the resultant SAPPHIRE (States And Pathways Projected with HIgh REsolution) plots provide a comprehensive picture of the thermodynamics and kinetics of complex, molecular systems exhibiting dynamics covering a range of time and length scales. Information on pathways connecting states and the level of recurrence are quickly inferred from the visualisation. The considerable advantages of our approach are speed and resolution: the SAPPHIRE plot is scalable to very large data sets and represents every single snapshot. This minimizes the risk of missing states because of overlap or prior coarse-graining of the data.

DOI10.1038/srep06264
pubindex

0190

Alternate JournalSci. Rep.
PubMed ID25179558
PubMed Central IDPMC4151098
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