A Massively Parallel CUDA Algorithm to Compute and Visualize the Solvent Excluded Surface for Dynamic Molecular Data

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dc.contributor.authorSchäfer, Marcoen_US
dc.contributor.authorKrone, Michaelen_US
dc.contributor.editorByska, Jan and Krone, Michael and Sommer, Björnen_US
dc.date.accessioned2019-06-02T18:25:23Z
dc.date.available2019-06-02T18:25:23Z
dc.date.issued2019
dc.description.abstractThe 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.en_US
dc.description.sectionheadersSession 1
dc.description.seriesinformationWorkshop on Molecular Graphics and Visual Analysis of Molecular Data
dc.identifier.doi10.2312/molva.20191094
dc.identifier.isbn978-3-03868-085-7
dc.identifier.pages1-9
dc.identifier.urihttps://doi.org/10.2312/molva.20191094
dc.identifier.urihttps://diglib.eg.org:443/handle/10.2312/molva20191094
dc.publisherThe Eurographics Associationen_US
dc.subjectHuman
dc.subjectcentered computing
dc.subjectVisualization
dc.subjectComputing methodologies
dc.subjectParallel algorithms
dc.subjectApplied computing
dc.subjectMolecular structural biology
dc.titleA Massively Parallel CUDA Algorithm to Compute and Visualize the Solvent Excluded Surface for Dynamic Molecular Dataen_US
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MolVa: Workshop on Molecular Graphics and Visual Analysis of Molecular Data 2019