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GPU Accelerated Molecular Surface Computing |
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PP: 185S-194S |
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Author(s) |
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Byungjoo Kim et al,
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Abstract |
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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 1/27 ×1/27× 1/27 of the original bounding box is obtained in
66.53ms on average. |
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