%0 Journal Article
%J Journal of Molecular Graphics and Modelling
%D 2008
%T Parallel, stochastic measurement of molecular surface area
%A Juba,Derek
%A Varshney, Amitabh
%K gpu
%K Molecular surface
%K Parallel
%K Progressive
%K Quasi-random
%K Stochastic
%X 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.
%B Journal of Molecular Graphics and Modelling
%V 27
%P 82 - 87
%8 2008/08//
%@ 1093-3263
%G eng
%U http://www.sciencedirect.com/science/article/pii/S1093326308000387
%N 1
%R 10.1016/j.jmgm.2008.03.001