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Author: Glennie Helles

Affiliation: University of Copenhagen, Denmark

Keyword(s): Protein structure prediction, Parallelism, Genetic algorithm, Parallel tempering.

Related Ontology Subjects/Areas/Topics: Bioinformatics ; Biomedical Engineering ; Structural Bioinformatics

Abstract: In attempts to predict the tertiary structure of proteins we use almost exclusively metaheuristics. However, despite known differences in performance of metaheuristics for different problems, the effect of the choice of metaheuristic has received precious little attention in this field. Particularly parallel implementations have been demonstrated to generally outperform their sequential counterparts, but they are nevertheless used to a much lesser extent for protein structure prediction. In this work we focus strictly on parallel algorithms for protein structure prediction and propose a parallel algorithm, which adds an iterative layer to the traditional niche genetic algorithm. We implement both the traditional niche genetic algorithm and the parallel tempering algorithm in a fashion that allows us to compare the algorithms and look at how they differ in performance. The results show that the iterative niche algorithm converges much faster at lower energy structures than both the tr aditional niche genetic algorithm and the parallel tempering algorithm. (More)

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Paper citation in several formats:
Helles, G. (2010). IMPROVING SEARCH FOR LOW ENERGY PROTEIN STRUCTURES WITH AN ITERATIVE NICHE GENETIC ALGORITHM. In Proceedings of the First International Conference on Bioinformatics (BIOSTEC 2010) - BIOINFORMATICS; ISBN 978-989-674-019-1; ISSN 2184-4305, SciTePress, pages 226-232. DOI: 10.5220/0002743702260232

@conference{bioinformatics10,
author={Glennie Helles.},
title={IMPROVING SEARCH FOR LOW ENERGY PROTEIN STRUCTURES WITH AN ITERATIVE NICHE GENETIC ALGORITHM},
booktitle={Proceedings of the First International Conference on Bioinformatics (BIOSTEC 2010) - BIOINFORMATICS},
year={2010},
pages={226-232},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0002743702260232},
isbn={978-989-674-019-1},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the First International Conference on Bioinformatics (BIOSTEC 2010) - BIOINFORMATICS
TI - IMPROVING SEARCH FOR LOW ENERGY PROTEIN STRUCTURES WITH AN ITERATIVE NICHE GENETIC ALGORITHM
SN - 978-989-674-019-1
IS - 2184-4305
AU - Helles, G.
PY - 2010
SP - 226
EP - 232
DO - 10.5220/0002743702260232
PB - SciTePress

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