A Massively Parallel CUDA Algorithm to Compute and Visualize the Solvent Excluded Surface for Dynamic Molecular Data

Schäfer, Marco; Krone, Michael

doi:10.2312/molva.20191094

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“…One important bottleneck that was lifted with approaches such as QuickSurf based on Gaussian surfaces is the capacity to generate such surfaces in real-time ( Krone et al, 2012 ). Similar approaches have been presented for the Solvent Excluded Surfaces (SES) ( Hermosilla et al, 2017a ; Martinez et al, 2019a ; Schäfer et al, 2019 ; Lindow et al, 2010 ) proposed various enhancements, based on a parallelization approach, aimed at reducing update times for the SES and the molecular skin surface (MSS) visualization.…”

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.

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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: 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.

View full text Add to dashboard Cite

show abstract

A Massively Parallel CUDA Algorithm to Compute and Visualize the Solvent Excluded Surface for Dynamic Molecular Data

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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