A memetic approach to protein structure prediction in triangular lattices

Authors:
Md. Kamrul Islam;Madhu Chetty;A. Dayem Ullah;K. Steinhöfel
Affiliations:
GSIT, Monash University, Churchill, VIC, Australia;GSIT, Monash University, Churchill, VIC, Australia;Department of Informatics, King's College London, London, UK;Department of Informatics, King's College London, London, UK
Venue:
ICONIP'11 Proceedings of the 18th international conference on Neural Information Processing - Volume Part I
Year:
2011

Citing 11
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Abstract

Protein structure prediction (PSP) remains one of the most challenging open problems in structural bioinformatics. Simplified models in terms of lattice structure and energy function have been proposed to ease the computational hardness of this combinatorial optimization problem. In this paper, we describe a clustered meme-based evolutionary approach for PSP using triangular lattice model. Under the framework of memetic algorithm, the proposed method extracts a pool of cultural information from different regions of the search space using data clustering technique. These highly observed local substructures, termed as meme, are then aggregated centrally for further refinements as second stage of evolution. The optimal utilization of ‘explore-and-exploit' feature of evolutionary algorithms is ensured by the inherent parallel architecture of the algorithm and subsequent use of cultural information.