GPU Accelerated Molecular Surface Computing

Byungjoo Kim, Ku-Jin Kim, Joon-Kyung Seong
Graduate School of Electronics, Kyungpook National University, 702-701 Daegu, Korea
Applied Mathematics & Information Sciences, Volume 6, No. 1S, pp. 185S-194S, 2012


   title={GPU Accelerated Molecular Surface Computing},

   author={Kim, B. and Kim, K.J. and Seong, J.K.},

   journal={Appl. Math},






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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.
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