Improved Umbrella Visualization implemented in UnityMol gives valuable insight on sugar/protein interplay

Besancon, Camille; Wong, Hua; Rao, Rajas M.; Dauchez, Manuel; Belloy, Nicolas; Jonquet, Jessica; Baud, Stéphanie

doi:10.2312/molva.20201097

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“…The UnityMol software has some coarse-grained specific features, such as visualization of secondary structure guides for proteins and nucleic acids, a functionality that most visualization tools currently lack for CG systems. (Besançon et al, 2020a;Besançon et al, 2020b), developed an original approach in which a shadow captures certain features of a molecular simulation. This umbrella visualization mode is a graphical method developed in the context of sugar simulations.…”

Section: Figure 10mentioning

confidence: 99%

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From complex data to clear insights: visualizing molecular dynamics trajectories

Belghit,

Spivak,

Dauchez

et al. 2024

Front. Bioinform.

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Advances in simulations, combined with technological developments in high-performance computing, have made it possible to produce a physically accurate dynamic representation of complex biological systems involving millions to billions of atoms over increasingly long simulation times. The analysis of these computed simulations is crucial, involving the interpretation of structural and dynamic data to gain insights into the underlying biological processes. However, this analysis becomes increasingly challenging due to the complexity of the generated systems with a large number of individual runs, ranging from hundreds to thousands of trajectories. This massive increase in raw simulation data creates additional processing and visualization challenges. Effective visualization techniques play a vital role in facilitating the analysis and interpretation of molecular dynamics simulations. In this paper, we focus mainly on the techniques and tools that can be used for visualization of molecular dynamics simulations, among which we highlight the few approaches used specifically for this purpose, discussing their advantages and limitations, and addressing the future challenges of molecular dynamics visualization.

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Section: Figure 10mentioning

confidence: 99%

“…( Besançon et al, 2020a ; Besançon et al, 2020b ), developed an original approach in which a shadow captures certain features of a molecular simulation. This umbrella visualization mode is a graphical method developed in the context of sugar simulations.…”

Section: General Considerations On Visualization Of Complex Molecular...mentioning

confidence: 99%

From complex data to clear insights: visualizing molecular dynamics trajectories

Belghit,

Spivak,

Dauchez

et al. 2024

Front. Bioinform.

Self Cite

View full text Add to dashboard Cite

show abstract

Improved Umbrella Visualization implemented in UnityMol gives valuable insight on sugar/protein interplay

Cited by 1 publication

References 0 publications

From complex data to clear insights: visualizing molecular dynamics trajectories

From complex data to clear insights: visualizing molecular dynamics trajectories

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