Parallel computation of solvent accessible surface area of protein molecules

E. Suh; B. K. Lee; R. Martino; B. Narahari; Alok Nidhi Choudhary

doi:10.1109/IPPS.1993.262798

Parallel computation of solvent accessible surface area of protein molecules

E. Suh, B. K. Lee, R. Martino, B. Narahari, Alok Nidhi Choudhary

Electrical and Computer Engineering

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

5 Scopus citations

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.

Original language	English (US)
Title of host publication	Proceedings of 7th International Parallel Processing Symposium, IPPS 1993
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	685-689
Number of pages	5
ISBN (Electronic)	0818634421, 9780818634420
DOIs	https://doi.org/10.1109/IPPS.1993.262798
State	Published - 1993
Event	7th International Parallel Processing Symposium, IPPS 1993 - Newport, United States Duration: Apr 13 1993 → Apr 16 1993

Publication series

Name	Proceedings of 7th International Parallel Processing Symposium, IPPS 1993

Conference

Conference	7th International Parallel Processing Symposium, IPPS 1993
Country/Territory	United States
City	Newport
Period	4/13/93 → 4/16/93

Funding

*This work supported in part by NSF grant CCR-9209345. This work supported in part by NSF grant CCR-9209345

ASJC Scopus subject areas

Computer Science Applications
Hardware and Architecture
Software
Computational Theory and Mathematics
Computer Networks and Communications

Access to Document

10.1109/IPPS.1993.262798

Cite this

Suh, E., Lee, B. K., Martino, R., Narahari, B., & Choudhary, A. N. (1993). Parallel computation of solvent accessible surface area of protein molecules. In Proceedings of 7th International Parallel Processing Symposium, IPPS 1993 (pp. 685-689). Article 262798 (Proceedings of 7th International Parallel Processing Symposium, IPPS 1993). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/IPPS.1993.262798

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title = "Parallel computation of solvent accessible surface area of protein molecules",

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.",

author = "E. Suh and Lee, {B. K.} and R. Martino and B. Narahari and Choudhary, {Alok Nidhi}",

note = "Funding Information: *This work supported in part by NSF grant CCR-9209345. Funding Information: This work supported in part by NSF grant CCR-9209345 Publisher Copyright: {\textcopyright} 1993 IEEE.; 7th International Parallel Processing Symposium, IPPS 1993 ; Conference date: 13-04-1993 Through 16-04-1993",

year = "1993",

doi = "10.1109/IPPS.1993.262798",

language = "English (US)",

series = "Proceedings of 7th International Parallel Processing Symposium, IPPS 1993",

publisher = "Institute of Electrical and Electronics Engineers Inc.",

pages = "685--689",

booktitle = "Proceedings of 7th International Parallel Processing Symposium, IPPS 1993",

address = "United States",

}

Suh, E, Lee, BK, Martino, R, Narahari, B & Choudhary, AN 1993, Parallel computation of solvent accessible surface area of protein molecules. in Proceedings of 7th International Parallel Processing Symposium, IPPS 1993., 262798, Proceedings of 7th International Parallel Processing Symposium, IPPS 1993, Institute of Electrical and Electronics Engineers Inc., pp. 685-689, 7th International Parallel Processing Symposium, IPPS 1993, Newport, United States, 4/13/93. https://doi.org/10.1109/IPPS.1993.262798

Parallel computation of solvent accessible surface area of protein molecules. / Suh, E.; Lee, B. K.; Martino, R. et al.
Proceedings of 7th International Parallel Processing Symposium, IPPS 1993. Institute of Electrical and Electronics Engineers Inc., 1993. p. 685-689 262798 (Proceedings of 7th International Parallel Processing Symposium, IPPS 1993).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

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AU - Martino, R.

AU - Narahari, B.

AU - Choudhary, Alok Nidhi

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Y1 - 1993

N2 - 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.

AB - 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.

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EP - 689

BT - Proceedings of 7th International Parallel Processing Symposium, IPPS 1993

PB - Institute of Electrical and Electronics Engineers Inc.

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Suh E, Lee BK, Martino R, Narahari B, Choudhary AN. Parallel computation of solvent accessible surface area of protein molecules. In Proceedings of 7th International Parallel Processing Symposium, IPPS 1993. Institute of Electrical and Electronics Engineers Inc. 1993. p. 685-689. 262798. (Proceedings of 7th International Parallel Processing Symposium, IPPS 1993). doi: 10.1109/IPPS.1993.262798

Parallel computation of solvent accessible surface area of protein molecules

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