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

Schäfer, Marco; Krone, Michael

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

Files

001-009.pdf (10.78 MB)

Date

2019

Authors

Schäfer, Marco
Krone, Michael

Publisher

The Eurographics Association

Abstract

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.

        @inproceedings{10.2312:molva.20191094
,
booktitle = {Workshop on Molecular Graphics and Visual Analysis of Molecular Data
},
editor = {Byska, Jan and Krone, Michael and Sommer, Björn
},
title = {{A Massively Parallel CUDA Algorithm to Compute and Visualize the Solvent Excluded Surface for Dynamic Molecular Data
}},
author = {Schäfer, Marco and 
Krone, Michael
},
year = {2019
},
publisher = {The Eurographics Association
},
ISBN = {978-3-03868-085-7
},
DOI = {10.2312/molva.20191094
}
}