GPU Accelerated Molecular Surface Computing
- Authors
- Kim, Byungjoo; Kim, Ku-Jin; Seong, Joon-Kyung
- Issue Date
- Jan-2012
- Publisher
- NATURAL SCIENCES PUBLISHING CORPORATION
- Keywords
- Molecular surface; solvent-excluded surface; offset; voxel map; GPU acceleration
- Citation
- APPLIED MATHEMATICS & INFORMATION SCIENCES, v.6, pp.185 - 194
- Journal Title
- APPLIED MATHEMATICS & INFORMATION SCIENCES
- Volume
- 6
- Start Page
- 185
- End Page
- 194
- URI
- http://scholarworks.bwise.kr/ssu/handle/2018.sw.ssu/12527
- ISSN
- 1935-0090
- 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 1/2(7) x1/2(7)x 1/2(7) of the original bounding box is obtained in 66.53ms on average.
- Files in This Item
- There are no files associated with this item.
- Appears in
Collections - College of Information Technology > School of Computer Science and Engineering > 1. Journal Articles
![qrcode](https://api.qrserver.com/v1/create-qr-code/?size=55x55&data=https://scholarworks.bwise.kr/ssu/handle/2018.sw.ssu/12527)
Items in ScholarWorks are protected by copyright, with all rights reserved, unless otherwise indicated.