<i>UnityMol</i> prototype for FAIR sharing of molecular-visualization experiences: from pictures in the cloud to collaborative virtual reality exploration in immersive 3D environments

Martinez, Xavier; Baaden, Marc

doi:10.1107/s2059798321002941

Cited by 19 publications

(22 citation statements)

References 28 publications

(27 reference statements)

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“…MDDriver allows the easy creation of a network socket between a molecular visualization user interface and a physics-based simulation engine. We use our own molecular visualization tool, UnityMol [23], to drive the dynamic behavior of the molecule in our IMPALA implementation. The relationship between these three software components is shown schematically in Figure 3 and uses standardized protocol and data structures for information exchange.…”

Section: Software Components For Integration Of Impala In An Interact...mentioning

confidence: 99%

Fast and Interactive Positioning of Proteins within Membranes

et al. 2022

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(1) Background: We developed an algorithm to perform interactive molecular simulations (IMS) of protein alignment in membranes, allowing on-the-fly monitoring and manipulation of such molecular systems at various scales. (2) Methods: UnityMol, an advanced molecular visualization software; MDDriver, a socket for data communication; and BioSpring, a Spring network simulation engine, were extended to perform IMS. These components are designed to easily communicate with each other, adapt to other molecular simulation software, and provide a development framework for adding new interaction models to simulate biological phenomena such as protein alignment in the membrane at a fast enough rate for real-time experiments. (3) Results: We describe in detail the integration of an implicit membrane model for Integral Membrane Protein And Lipid Association (IMPALA) into our IMS framework. Our implementation can cover multiple levels of representation, and the degrees of freedom can be tuned to optimize the experience. We explain the validation of this model in an interactive and exhaustive search mode. (4) Conclusions: Protein positioning in model membranes can now be performed interactively in real time.

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Section: Software Components For Integration Of Impala In An Interact...mentioning

confidence: 99%

Fast and Interactive Positioning of Proteins within Membranes

et al. 2022

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“…In our world, and with our visual system, we are unable to see cells directly, but we use many techniques to obtain information on the cellular world. The challenge of representing them has been faced and solved with many creative tools for about 60 year, from cardboard models [ 11 ] to virtual reality [ 12 ]. However, most of these efforts have been made in an uncoordinated way, and we have now a range of visualization methods and styles.…”

Section: Coloring Biologymentioning

confidence: 99%

“…Technical aspects have also to be considered, in particular in relation the means of delivery (printed on paper, video/film, interactive video, even physical models [ 18 ] and Virtual reality [ 12 ]). This is likely to require detailed discussions, depending on what precisely we will aim at showing, and how it is defined or calculated.…”

Section: Coloring Biologymentioning

confidence: 99%

Colors in the representation of biological structures

Zoppé

2022

Journal of Integrative Bioinformatics

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Among the many properties of proteins, sugars, nucleic acids, membranes and other cellular components, color is not present. At the same time, we humans have a natural ability of recognizing and appreciating colors, and use them generously, with the aim of both delivering information and pleasing the eyes. In this article, I suggest how we can conciliate these two situations, with the contribution of biologists, artists, and computer graphics and perception experts. The concept can be developed in a series of initiatives involving the community, including discussion sessions, technical challenges, experimental studies and outreach activities.

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“…The MDsrv was the first tool that made interactive streaming and visualization of MD trajectories in web browsers more accessible ( 10 ); others followed including HTMoL ( 11 ), UnityMol ( 12 ), PCAViz ( 13 ) and 3dRS ( 14 ). The applications of these tools are broad, and they all cover the same functionalities of in-browser visualization and sharing of remote data.…”

Section: Introductionmentioning

confidence: 99%

MDsrv: visual sharing and analysis of molecular dynamics simulations

Philipp

Staritzbichler

Hernández

et al. 2022

Nucleic Acids Research

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Molecular dynamics simulation is a proven technique for computing and visualizing the time-resolved motion of macromolecules at atomic resolution. The MDsrv is a tool that streams MD trajectories and displays them interactively in web browsers without requiring advanced skills, facilitating interactive exploration and collaborative visual analysis. We have now enhanced the MDsrv to further simplify the upload and sharing of MD trajectories and improve their online viewing and analysis. With the new instance, the MDsrv simplifies the creation of sessions, which allows the exchange of MD trajectories with preset representations and perspectives. An important innovation is that the MDsrv can now access and visualize trajectories from remote datasets, which greatly expands its applicability and use, as the data no longer needs to be accessible on a local server. In addition, initial analyses such as sequence or structure alignments, distance measurements, or RMSD calculations have been implemented, which optionally support visual analysis. Finally, based on Mol*, MDsrv now provides faster and more efficient visualization of even large trajectories compared to its predecessor tool NGL.

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UnityMol prototype for FAIR sharing of molecular-visualization experiences: from pictures in the cloud to collaborative virtual reality exploration in immersive 3D environments

Cited by 19 publications

References 28 publications

Fast and Interactive Positioning of Proteins within Membranes

Fast and Interactive Positioning of Proteins within Membranes

Colors in the representation of biological structures

MDsrv: visual sharing and analysis of molecular dynamics simulations

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