MolVa: Workshop on Molecular Graphics and Visual Analysis of Molecular Data

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Browsing MolVa: Workshop on Molecular Graphics and Visual Analysis of Molecular Data by Subject "centered computing"

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    A Massively Parallel CUDA Algorithm to Compute and Visualize the Solvent Excluded Surface for Dynamic Molecular Data
    (The Eurographics Association, 2019) Schäfer, Marco; Krone, Michael; Byska, Jan and Krone, Michael and Sommer, Björn
    The interactive visualization of molecular surfaces can help users to understand the dynamic behavior of proteins in molecular dynamics simulations. These simulations play an important role in biochemical and pharmaceutical research, e.g. in drug design. The efficient calculation of molecular surfaces in a fast and memory-saving way is a challenging task. For example, to gain a detailed understanding of complex diseases like Alzheimer, conformational changes and spatial interactions between molecules have to be investigated. Molecular surfaces, such as Solvent Excluded Surfaces (SES), are instrumental for identifying structures such as tunnels or cavities that critically influence transport processes and docking events, which might induce enzymatic reactions. Therefore, we developed a highly parallelized algorithm that exploits the massive computing power of modern graphics hardware. Our analytical algorithm is suitable for the real-time computation of dynamic SES based on many time steps, as it runs interactively on a single consumer GPU for more than 20 k atoms.
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    A Virtual and Mixed Reality Platform for Molecular Design & Drug Discovery - Nanome Version 1.24
    (The Eurographics Association, 2023) Bennie, Simon J.; Maritan, Martina; Gast, Jonathon; Loschen, Marc; Gruffat, Daniel; Bartolotta, Roberta; Hessenauer, Sam; Leija, Edgardo; McCloskey, Steve; Byška, Jan; Krone, Michael; Sommer, Björn
    The success of the design and improvement of nanoscale biomolecules like proteins and small molecule drugs relies on a proper understanding of their three-dimensional structures. Nanome's virtual reality/mixed reality (VR/MR) platform provides an immersive and collaborative environment that offers a unique view into the nanoscale world. The platform enables faster and more effective ideation, improved communication of scientific concepts, and multiple tools for lead optimization of molecules. The latest 1.24 version of the Nanome platform integrates multi-user collaboration, mixed reality, enhanced avatars, and a flexible Python API for easy integration with various modeling techniques. We describe key elements of this state-of-the-art framework and how it can accelerate the pace of discovery through empowering industry-standard algorithms across domains of digital science. Nanome is available for download at https://home.nanome.ai/setup.