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01-Applied Mathematics & Information Sciences
An International Journal
               
 
 
 
 
 
 
 
 
 
 
 
 
 

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Volumes > Volume 06 > No. 6-1S

 
   

GPU Accelerated Molecular Surface Computing

PP: 185S-194S
Author(s)
Byungjoo Kim et al,
Abstract
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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