Title :
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
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;
Conference_Titel :
Parallel Processing Symposium, 1993., Proceedings of Seventh International
Conference_Location :
Newport, CA
Print_ISBN :
0-8186-3442-1
DOI :
10.1109/IPPS.1993.262798
