A Hybrid Local Search for Simplified Protein Structure Prediction
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Newton, MA Hakim
Duc, Nghia Pham
Sattar, Abdul
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Fernandes, P
SoleCasals, J
Fred, A
Gamboa, H
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Barcelona, SPAIN
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Abstract
Protein structure prediction based on Hydrophobic-Polar energy model essentially becomes searching for a conformation having a compact hydrophobic core at the center. The hydrophobic core minimizes the interaction energy between the amino acids of the given protein. Local search algorithms can quickly find very good conformations by moving repeatedly from the current solution to its "best" neighbor. However, once such a compact hydrophobic core is found, the search stagnates and spends enormous effort in quest of an alternative core. In this paper, we attempt to restructure segments of a conformation with such compact core. We select one large segment or a number of small segments and apply exhaustive local search. We also apply a mix of heuristics so that one heuristic can help escape local minima of another. We evaluated our algorithm by using Face Centered Cubic (FCC) Lattice on a set of standard benchmark proteins and obtain significantly better results than that of the state-of-the-art methods.
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BIOINFORMATICS 2013: PROCEEDINGS OF THE INTERNATIONAL CONFERENCE ON BIOINFORMATICS MODELS, METHODS AND ALGORITHMS
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© 2013 Springer Berlin/Heidelberg. This is the author-manuscript version of this paper. Reproduced in accordance with the copyright policy of the publisher.The original publication is available at www.springerlink.com
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Artificial intelligence not elsewhere classified