GPU Accelerated Molecular Surface Computing
Graduate School of Electronics, Kyungpook National University, 702-701 Daegu, Korea
Applied Mathematics & Information Sciences, Volume 6, No. 1S, pp. 185S-194S, 2012
@article{kim2012gpu,
title={GPU Accelerated Molecular Surface Computing},
author={Kim, B. and Kim, K.J. and Seong, J.K.},
journal={Appl. Math},
volume={6},
number={1S},
pages={185S–194S},
year={2012}
}
A method is presented for computing the SES (solvent excluded surface) of a protein molecule in interactive-time based on GPU (graphics processing unit) acceleration. First, the offset surface of the van der Waals spheres is sampled using an offset distance d that corresponds to the radius of the solvent probe. The SES is then constructed by extracting the surface at distance d from the sample points. For interactive-time computing, two space partitioning schemes are used, a voxel map and kd-tree, with data parallel schemes accelerated by GPU. In experiments using an average 1,848 atoms, a SES with a resolution of 1/2^7×1/2^7×1/2^7 of the original bounding box is obtained in 66.53ms on average.
February 26, 2012 by hgpu
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