Improving search for low energy protein structures with an iterative niche genetic algorithm

Glennie Helles*

*Corresponding author af dette arbejde

Publikation: Bidrag til bog/antologi/rapportKonferencebidrag i proceedingsForskningpeer review

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 traditional niche genetic algorithm and the parallel tempering algorithm.

OriginalsprogEngelsk
TitelProceedings of the First International Conference on Bioinformatics
Antal sider7
Vol/bind1
ForlagSCITEPRESS Digital Library
Publikationsdato2010
Sider226-232
ISBN (Trykt)978-989-674-019-1
DOI
StatusUdgivet - 2010
Begivenhed1st International Conference on Bioinformatics - Valencia, Spanien
Varighed: 20 jan. 201023 jan. 2010
Konferencens nummer: 1

Konference

Konference1st International Conference on Bioinformatics
Nummer1
Land/OmrådeSpanien
ByValencia
Periode20/01/201023/01/2010

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