Parallel computation of solvent accessible surface area of protein molecules

Author

Suh, E. ; Lee, B.K. ; Martino, R. ; Narahari, B. ; Choudhary, A.

Author_Institution

Nat. Inst. of Health, Bethesda, MD, USA

fYear

1993

fDate

13-16 Apr 1993

Firstpage

685

Lastpage

689

Abstract

The paper presents a parallel algorithm for computation of solvent accessible surface area of a molecule according to the Lee and Richards´s (1971) algorithm. The efficient parallelization of this process is crucial in dynamic simulations of protein molecules and protein folding studies. The solvent accessible surface area (ASA) problem exhibits inherent parallelism that is exploited in the design of a parallel program which is implemented on an Intel iPSC machine. The performance of the parallel algorithm is enhanced by a dynamic load balancing scheme. The authors report on experiments performed on a set of protein structures

Keywords

chemistry computing; digital simulation; parallel algorithms; proteins; Intel iPSC machine; dynamic load balancing; dynamic simulations; parallel algorithm; parallelization; protein folding; protein molecules; protein structures; solvent accessible surface area; Algorithm design and analysis; Atomic measurements; Computational modeling; Concurrent computing; Load management; Parallel algorithms; Partitioning algorithms; Proteins; Solvents; Stability;

fLanguage

English

Publisher

ieee

Conference_Titel

Parallel Processing Symposium, 1993., Proceedings of Seventh International

Conference_Location

Newport, CA

Print_ISBN

0-8186-3442-1

Type

conf

DOI

10.1109/IPPS.1993.262798

Filename

262798