ArticleScientific reports2014
High-resolution visualisation of the states and pathways sampled in molecular dynamics simulations.
Article in Scientific reports, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- A FAIR-Compliant Management Solution for Molecular Simulation Trajectories.Journal of chemical information and modeling · 2025Article
- Disrupting Dimeric β-Amyloid by Electric Fields.ACS physical chemistry Au · 2023Article
- Decrypting Integrins by Mixed-Solvent Molecular Dynamics Simulations.Journal of chemical information and modeling · 2023Article
- Molecular dynamics analysis of the structural properties of the transglutaminases ofComputational and structural biotechnology journal · 2022Article
- The ATAD2 bromodomain binds different acetylation marks on the histone H4 in similar fuzzy complexes.The Journal of biological chemistry · 2017Article
- Peptide Binding to a PDZ Domain by Electrostatic Steering via Nonnative Salt Bridges.Biophysical journal · 2015Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
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