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Parallel evolution strategy on grids for the protein threading problem
Authors:Alioune  
Affiliation:aSchool of Computer Science, 5115 Lambton Tower, University of Windsor, 401 Sunset Avenue, N9B 3P4, Windsor, Ont., Canada
Abstract: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.
Keywords:Protein  Threading  Three-dimensional structure  Fold  Energy  Alignment  Prediction  Evolution
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