Parallel, stochastic measurement of molecular surface area |
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Authors: | Juba Derek Varshney Amitabh |
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Affiliation: | aDepartment of Computer Science, University of Maryland, 4406 A.V. Williams Building, College Park, MD 20742, United States |
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Abstract: | Biochemists often wish to compute surface areas of proteins. A variety of algorithms have been developed for this task, but they are designed for traditional single-processor architectures. The current trend in computer hardware is towards increasingly parallel architectures for which these algorithms are not well suited.We describe a parallel, stochastic algorithm for molecular surface area computation that maps well to the emerging multi-core architectures. Our algorithm is also progressive, providing a rough estimate of surface area immediately and refining this estimate as time goes on. Furthermore, the algorithm generates points on the molecular surface which can be used for point-based rendering.We demonstrate a GPU implementation of our algorithm and show that it compares favorably with several existing molecular surface computation programs, giving fast estimates of the molecular surface area with good accuracy. |
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Keywords: | Molecular surface Parallel Progressive GPU Stochastic Quasi-random |
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