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Coarse-Grained Parallelization of Distance-Bound Smoothing for the Molecular Conformation Problem

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Book cover Distributed Computing (IWDC 2002)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2571))

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Abstract

Determining the three-dimensional structure of proteins is crucial to efficient drug design and understanding biological processes. One successful method for computing the molecule’s shape relies on the inter-atomic distance bounds provided by the Nucleo-Magnetic Resonance (NMR) spectroscopy. The accuracy of computed structures as well as the time required to obtain them are greatly improved if the gaps between the upper and lower distance-bounds are reduced. These gaps are reduced most effectively by applying the tetrangle inequality, derived from the Cayley-Menger determinant, to all atom-quadruples. However, tetrangle-inequality bound-smoothing is an extremely computation intensive task, requiring O(n 4) time for an n-atom molecule. To reduce the computation time, we propose a novel coarse-grained parallel algorithm intended for a Beowulf-type cluster of PCs. The algorithm employs p n/6 processors and requires O(n 4/p) time and O(p 2) communications. The number of communications is at least an order of magnitude lower than in the earlier parallelizations. Our implementation utilized the processors with at least 59% efficiency (including the communication overhead) — an impressive figure for a nonembarrassingly parallel problem on a cluster of workstations.

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Author information

Authors and Affiliations

  1. School of Electrical Engineering and Computer Science, University of Central Florida, 32816-2362, Orlando, FL

    Narsingh Deo & Paulius Micikevicius

Authors
  1. Narsingh Deo
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  2. Paulius Micikevicius
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Editor information

Editors and Affiliations

  1. Department of Computer Science and Engineering, University of Texas at Arlington Center for Research in Wireless Mobility and Networking (CReWMaN), P.O. Box 19015, 76019-0015, Arlington, TX, USA

    Sajal K. Das

  2. Department of Computer Science and Engineering, Jadavpur University, 700 032, Calcutta

    Swapan Bhattacharya

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© 2002 Springer-Verlag Berlin Heidelberg

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Deo, N., Micikevicius, P. (2002). Coarse-Grained Parallelization of Distance-Bound Smoothing for the Molecular Conformation Problem. In: Das, S.K., Bhattacharya, S. (eds) Distributed Computing. IWDC 2002. Lecture Notes in Computer Science, vol 2571. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-36385-8_6

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  • DOI: https://doi.org/10.1007/3-540-36385-8_6

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-00355-7

  • Online ISBN: 978-3-540-36385-9

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