QuickSES: A Library for Fast Computation of Solvent Excluded Surfaces

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dc.contributor.authorMartinez, Xavieren_US
dc.contributor.authorKrone, Michaelen_US
dc.contributor.authorBaaden, Marcen_US
dc.contributor.editorByska, Jan and Krone, Michael and Sommer, Björnen_US
dc.date.accessioned2019-06-02T18:25:25Z
dc.date.available2019-06-02T18:25:25Z
dc.date.issued2019
dc.description.abstractRecently, 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.en_US
dc.description.sectionheadersSession 2
dc.description.seriesinformationWorkshop on Molecular Graphics and Visual Analysis of Molecular Data
dc.identifier.doi10.2312/molva.20191095
dc.identifier.isbn978-3-03868-085-7
dc.identifier.pages11-15
dc.identifier.urihttps://doi.org/10.2312/molva.20191095
dc.identifier.urihttps://diglib.eg.org:443/handle/10.2312/molva20191095
dc.publisherThe Eurographics Associationen_US
dc.subjectApplied computing
dc.subjectMolecular structural biology
dc.subjectComputing methodologies
dc.subjectMassively parallel algorithms
dc.titleQuickSES: A Library for Fast Computation of Solvent Excluded Surfacesen_US
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MolVa: Workshop on Molecular Graphics and Visual Analysis of Molecular Data 2019