Browsing by Author "Baaden, Marc"

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    QuickSES: A Library for Fast Computation of Solvent Excluded Surfaces
    (The Eurographics Association, 2019) Martinez, Xavier; Krone, Michael; Baaden, Marc; Byska, Jan and Krone, Michael and Sommer, Björn
    Recently, several fast methods to compute Solvent Excluded Surfaces (SES) on GPUs have been presented. While these published methods reportedly yield interesting and useful results, up to now no public, freely accessible implementation of a fast and opensource SES mesh computation method that runs on GPUs is available. Most molecular viewers, therefore, still use legacy CPU methods that run only on a single core, without GPU acceleration. In this paper, we present an in-depth explanation and a fully open-source CUDA implementation of the fast, grid-based computation method proposed by Hermosilla et al. [HKG*17]. Our library called QuickSES runs on GPUs and is distributed with a permissive license. It comes with a standalone program that reads Protein Data Bank (PDB) files and outputs a complete SES mesh as a Wavefront OBJ file. Alternatively it can directly be integrated in classical molecular viewers as shared library. We demonstrate the low memory consumption to enable execution on lower-end GPUs, and compare the runtime speed-up to available state-of-the-art tools.
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    State of the Art of Molecular Visualization in Immersive Virtual Environments
    (© 2023 Eurographics ‐ The European Association for Computer Graphics and John Wiley & Sons Ltd., 2023) Kuťák, David; Vázquez, Pere‐Pau; Isenberg, Tobias; Krone, Michael; Baaden, Marc; Byška, Jan; Kozlíková, Barbora; Miao, Haichao; Hauser, Helwig and Alliez, Pierre
    Visualization plays a crucial role in molecular and structural biology. It has been successfully applied to a variety of tasks, including structural analysis and interactive drug design. While some of the challenges in this area can be overcome with more advanced visualization and interaction techniques, others are challenging primarily due to the limitations of the hardware devices used to interact with the visualized content. Consequently, visualization researchers are increasingly trying to take advantage of new technologies to facilitate the work of domain scientists. Some typical problems associated with classic 2D interfaces, such as regular desktop computers, are a lack of natural spatial understanding and interaction, and a limited field of view. These problems could be solved by immersive virtual environments and corresponding hardware, such as virtual reality head‐mounted displays. Thus, researchers are investigating the potential of immersive virtual environments in the field of molecular visualization. There is already a body of work ranging from educational approaches to protein visualization to applications for collaborative drug design. This review focuses on molecular visualization in immersive virtual environments as a whole, aiming to cover this area comprehensively. We divide the existing papers into different groups based on their application areas, and types of tasks performed. Furthermore, we also include a list of available software tools. We conclude the report with a discussion of potential future research on molecular visualization in immersive environments.