title: Parallel, stochastic measurement of molecular surface area.
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.
authors.affiliation: Department of Computer Science, University of Maryland, College Park, MD 20742, United States. juba@cs.umd.edu
authors.forename: Derek
authors.initials: D
authors.lastname: Juba
authors.forename: Amitabh
authors.initials: A
authors.lastname: Varshney
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry; D013269:Stochastic Processes; D013499:Surface Properties; D013997:Time Factors
chemical_list: D011506:Proteins