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

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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.

Table of contents conference proceedings

The tables of contents are generated automatically and are based on the data records of the individual contributions available in the index of the TIB portal. The display of the Tables of Contents may therefore be incomplete.

1
A Massively Parallel CUDA Algorithm to Compute and Visualize the Solvent Excluded Surface for Dynamic Molecular Data
Schäfer, Marco / Krone, Michael | 2019
11
QuickSES: A Library for Fast Computation of Solvent Excluded Surfaces
Martinez, Xavier / Krone, Michael / Baaden, Marc | 2019
17
MolFind - Integrated Multi-Selection Schemes for Complex Molecular Structures
Skånberg, Robin / Linares, Mathieu / Falk, Martin / Hotz, Ingrid / Ynnerman, Anders | 2019
23
PBmapclust: Mapping and Clustering the Protein Conformational Space Using a Structural Alphabet
Vetrivel, Iyanar / Hoffmann, Lionel / Guegan, Sean / Offmann, Bernard / Laurent, Adele D. | 2019
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