On the approximation of protein threading
Theoretical Computer Science - Special issue: Genome informatics
Genetic Algorithms in Search, Optimization and Machine Learning
Genetic Algorithms in Search, Optimization and Machine Learning
Constraints
Parallel Computation in Biological Sequence Analysis
IEEE Transactions on Parallel and Distributed Systems
Genetic Algorithms for Protein Threading
ISMB '98 Proceedings of the 6th International Conference on Intelligent Systems for Molecular Biology
Solving the Protein Threading Problem in Parallel
IPDPS '03 Proceedings of the 17th International Symposium on Parallel and Distributed Processing
Parallel divide and conquer approach for the protein threading problem: Research Articles
Concurrency and Computation: Practice & Experience - High Performance Computational Biology
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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.