Parallel, stochastic measurement of molecular surface area

TitleParallel, stochastic measurement of molecular surface area
Publication TypeJournal Articles
Year of Publication2008
AuthorsJuba D, Varshney A
JournalJournal of Molecular Graphics and Modelling
Pagination82 - 87
Date Published2008/08//
ISBN Number1093-3263
Keywordsgpu, Molecular surface, Parallel, Progressive, Quasi-random, Stochastic

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.