TY - GEN
T1 - Efficient algorithms for protein solvent accessible surface area
AU - Futamura, N.
AU - Aluru, S.
AU - Ranjan, D.
AU - Mehrotra, K.
N1 - Publisher Copyright:
© 2000 IEEE.
PY - 2000
Y1 - 2000
N2 - We present faster sequential and parallel algorithms for computing the solvent accessible surface area (ASA) of protein molecules. The ASA can be obtained by calculating the exposed surface area of the spheres obtained by increasing the van der Waals' radii of the atoms with the van der Waals' radius of the solvent. Using domain specific knowledge, we show that the number of sphere intersections is O(n) and present algorithms to compute the same in O(nlogn) sequential time and O(nlogn/p) parallel time, where n is the number of atoms and p is the number of processors. We also present a heuristic based on space-filling curves to improve performance in practice. These are significant improvements over previously known algorithms which take Ω(n2) time sequentially and Ω(n2/p) time in parallel. While existing parallel algorithms achieve their run-time by dynamic load balancing, our algorithms are faster and do not need load balancing.
AB - We present faster sequential and parallel algorithms for computing the solvent accessible surface area (ASA) of protein molecules. The ASA can be obtained by calculating the exposed surface area of the spheres obtained by increasing the van der Waals' radii of the atoms with the van der Waals' radius of the solvent. Using domain specific knowledge, we show that the number of sphere intersections is O(n) and present algorithms to compute the same in O(nlogn) sequential time and O(nlogn/p) parallel time, where n is the number of atoms and p is the number of processors. We also present a heuristic based on space-filling curves to improve performance in practice. These are significant improvements over previously known algorithms which take Ω(n2) time sequentially and Ω(n2/p) time in parallel. While existing parallel algorithms achieve their run-time by dynamic load balancing, our algorithms are faster and do not need load balancing.
UR - http://www.scopus.com/inward/record.url?scp=77950960729&partnerID=8YFLogxK
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U2 - 10.1109/HPC.2000.843502
DO - 10.1109/HPC.2000.843502
M3 - Conference contribution
AN - SCOPUS:77950960729
T3 - Proceedings - 4th International Conference/Exhibition on High Performance Computing in the Asia-Pacific Region, HPC-Asia 2000
SP - 586
EP - 592
BT - Proceedings - 4th International Conference/Exhibition on High Performance Computing in the Asia-Pacific Region, HPC-Asia 2000
PB - Institute of Electrical and Electronics Engineers Inc.
T2 - 4th International Conference/Exhibition on High Performance Computing in the Asia-Pacific Region, HPC-Asia 2000
Y2 - 14 May 2000 through 17 May 2000
ER -