GPU-powered tools boost molecular visualization

Chavent, Matthieu; Lévy, Bruno; Krone, Michael; Bidmon, Katrin; Nominé, Jean-Philippe; Ertl, Thomas; Baaden, Marc

doi:10.1093/bib/bbq089

Cited by 42 publications

(41 citation statements)

References 32 publications

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“…So, the latest contributions from this domain of research has clearly helped scientists to display more and more complex systems. The latest graphics techniques can provide an improved visual perception which could drastically impact the way to visualize molecular structures [Chavent, Lévy, Krone, Bidmon, Nominé, Ertl & Baaden (2011)]. For example, using GPU shaders, i.e.…”

Section: Gpu Shaders and Hyperballsmentioning

confidence: 99%

Advances in Human-Protein Interaction - Interactive and Immersive Molecular Simulations

Tek¹,

Chavent²,

Baaden³

et al. 2012

Protein-Protein Interactions - Computational and Experimental Tools

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Section: Gpu Shaders and Hyperballsmentioning

confidence: 99%

Advances in Human-Protein Interaction - Interactive and Immersive Molecular Simulations

Tek¹,

Chavent²,

Baaden³

et al. 2012

Protein-Protein Interactions - Computational and Experimental Tools

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“…Molecular structure visualization. A lot of research has been conducted to improve visualization of complex molecular structures [23,12,53,5,18,39]. As discussing all these techniques would be beyond the scope of this paper, we refer the interested reader to the state-of-the-art report by Kozlíková et al [26], and only focus on those techniques directly related to the visualizations proposed in this paper.…”

Section: Related Workmentioning

confidence: 99%

Physics-Based Visual Characterization of Molecular Interaction Forces

Hermosilla

Estrada

Guallar

et al. 2017

IEEE Trans. Visual. Comput. Graphics

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Fig. 1. Successive steps during the visual analysis of the binding nature of Aspirin and the Phospholipase A2 protein. We compute and visualize all essential interaction energies represented by 2D and 3D arrows. The orientation of the depicted arrows encodes the sign of the energy, i.e., attracting vs. repelling force. The width of the arrows as well as the color of the residue's silhouettes support energy quantification. During the visual analysis, energies are computed and depicted on-the-fly to support interactive hypothesis testing (left), and residues can be filtered based on energy and distance to obtain a more focused view (middle). Additionally, a 2D visualization helps to obtain total energy values in an uncluttered manner (right).Abstract-Molecular simulations are used in many areas of biotechnology, such as drug design and enzyme engineering. Despite the development of automatic computational protocols, analysis of molecular interactions is still a major aspect where human comprehension and intuition are key to accelerate, analyze, and propose modifications to the molecule of interest. Most visualization algorithms help the users by providing an accurate depiction of the spatial arrangement: the atoms involved in inter-molecular contacts. There are few tools that provide visual information on the forces governing molecular docking. Unfortunately these tools, commonly restricted to close interaction between atoms, do not consider whole simulation paths, long-range distances and, importantly, do not provide visual cues for a quicker and intuitive comprehension of the energy functions (modeling intermolecular interactions) involved. In this paper, we propose visualizations designed to enable the characterization of interaction forces by taking into account several relevant variables such as molecule-ligand distance and the energy function, which is essential to understand binding affinities. We put emphasis on mapping molecular docking paths obtained from Molecular Dynamics or Monte Carlo simulations, and provide time-dependent visualizations for different energy components and particle resolutions: atoms, groups or residues. The presented visualizations have the potential to support domain experts in a more efficient drug or enzyme design process.

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“…Besides the challenges related to communicating complex molecular structures [6,14,16,19,21,47], visualization algorithms need to be able to show the composition of elements and the various reactions that happen in simulations. In the following, we classify the methods described in literature into two groups: methods tailored to comprehend atomic structures and methods for illustrating molecular reactions.…”

Section: Related Workmentioning

confidence: 99%

Real-Time Molecular Visualization Supporting Diffuse Interreflections and Ambient Occlusion

Skånberg

Vázquez

Guallar

et al. 2016

IEEE Trans. Visual. Comput. Graphics

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(a) Time step 1 (b) Time step 2 (c) Time step 3 Fig. 1. By deriving analytic expressions, we can enhance molecular visualizations and realize interreflections in real-time. The images (a-c) show three time steps of a molecular simulation investigating the interaction between a magenta-colored ligand and a receptor molecule, which receives exaggerated diffuse interreflections. Due to these interreflections it can be seen how the ligand enters the active site.Abstract-Today molecular simulations produce complex data sets capturing the interactions of molecules in detail. Due to the complexity of this time-varying data, advanced visualization techniques are required to support its visual analysis. Current molecular visualization techniques utilize ambient occlusion as a global illumination approximation to improve spatial comprehension. Besides these shadow-like effects, interreflections are also known to improve the spatial comprehension of complex geometric structures. Unfortunately, the inherent computational complexity of interreflections would forbid interactive exploration, which is mandatory in many scenarios dealing with static and time-varying data. In this paper, we introduce a novel analytic approach for capturing interreflections of molecular structures in real-time. By exploiting the knowledge of the underlying space filling representations, we are able to reduce the required parameters and can thus apply symbolic regression to obtain an analytic expression for interreflections. We show how to obtain the data required for the symbolic regression analysis, and how to exploit our analytic solution to enhance interactive molecular visualizations.

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GPU-powered tools boost molecular visualization

Cited by 42 publications

References 32 publications

Advances in Human-Protein Interaction - Interactive and Immersive Molecular Simulations

Advances in Human-Protein Interaction - Interactive and Immersive Molecular Simulations

Physics-Based Visual Characterization of Molecular Interaction Forces

Real-Time Molecular Visualization Supporting Diffuse Interreflections and Ambient Occlusion

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