2014
DOI: 10.1038/srep06264
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High-Resolution Visualisation of the States and Pathways Sampled in Molecular Dynamics Simulations

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… Show more

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Cited by 19 publications
(33 citation statements)
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“…Different annotations of the trajectory can be plotted per snapshot as arranged by the progress index to obtain a SAP-PHIRE plot (48), which helps in the interpretation of the discovered basins. The cut function we show here for kinetic partitioning is the so-called local cut in the original publication (49).…”
Section: Discussionmentioning
confidence: 99%
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“…Different annotations of the trajectory can be plotted per snapshot as arranged by the progress index to obtain a SAP-PHIRE plot (48), which helps in the interpretation of the discovered basins. The cut function we show here for kinetic partitioning is the so-called local cut in the original publication (49).…”
Section: Discussionmentioning
confidence: 99%
“…To quantify the mutual similarity and level of overlap between the apo-and holo-runs, we turn to a powerful analysis and visualization strategy called a SAPPHIRE plot (48). Briefly, all snapshots are arranged by geometric criteria that use as the only input a definition of pairwise distance between conformations.…”
Section: Holo-trajectories Return To the Crystallographic Structures mentioning
confidence: 99%
“…Recently, we have developed an algorithm for the analysis of long MD trajectories (46,47). The resulting SAPPHIRE (States And Pathways Projected with HIgh REsolution) plot is a comprehensive visualization of the thermodynamics and kinetics of the simulated system.…”
Section: Sapphire Plotmentioning
confidence: 99%
“…Table S1 in the Supporting Material contains the full list of atom pairs used. We briefly describe the method here and refer the reader to the original publications for more details (46,47). Starting from an arbitrary snapshot, all the snapshots are sequentially ordered in a stepwise fashion.…”
Section: Sapphire Plotmentioning
confidence: 99%
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