Parallel, stochastic measurement of molecular surface area

D. Juba, A. Varshney
Department of Computer Science, University of Maryland, 4406 A.V. Williams Building, College Park, MD 20742, United States
Journal of Molecular Graphics and Modelling, Vol. 27, No. 1. (August 2008), pp. 82-87.


   title={Parallel, stochastic measurement of molecular surface area},

   author={Juba, D. and Varshney, A.},

   journal={Journal of Molecular Graphics and Modelling},








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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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