Parallel evolution strategy on grids for the protein threading problem

doi:10.1016/j.jpdc.2006.08.005

2006-12-01

PRE

Alioune Ngom *

DOI：10.1016/j.jpdc.2006.08.005

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The protein threading problem is the problem of determining the three-dimensional structure of a given but arbitrary protein sequence from a set of known structures of other proteins. This problem is known to be NP-hard and current computational approaches to threading are unrealistic for long proteins and/or large template data sets. In this paper, we propose an evolution strategy for the solution of the protein threading problem. We also propose three parallel methods for fast threading. Our experiments produced encouraging preliminary results in term of threading energy as well as significant reduction in threading time. (C) 2006 Elsevier Inc. All rights reserved.

Keyword:

protein

threading

three-dimensional structure

fold

energy

alignment

prediction

evolution

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Journal of Parallel and Distributed Computing

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