Visual exploration of large normal mode spaces to study protein flexibility

Bedoucha, Pierre; Reuter, Nathalie; Hauser, Helwig

doi:10.1016/j.cag.2020.05.025

Cited by 8 publications

(2 citation statements)

References 46 publications

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“…In 2020, ( Bedoucha et al, 2020 ), investigated protein function through an interactive visualization approach to reduce and explore the vast data space. This method enables the deduction of pertinent protein function by analyzing the dynamics of a single structure through protein tunneling analysis, taking into account combinations of normal modes that span the entire normal mode space.…”

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

“…Consequently, we accepted the six papers that are now collected in this special section. The section includes a survey on medical animation, covering applications in medical education, diagnosis, treatment planning and forensics [1] , one paper that proposes a novel approach for the visual exploration of large normal mode spaces to study protein flexibility [2] , one paper presenting a complete system for the data extraction and visual exploration of colon contents and morphological data [3] , and three visual analytics papers, addressing the exploration and analysis of pelvic organ variability in cohorts of patients undergoing radiotherapy [4] , the interactive exploration of metabolite signatures in MR spectroscopy studies [5] , and explainability in clinical decision support, inspired by decision making within clinical routine [6] .…”

Section: Computers and Graphicsmentioning

confidence: 99%