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Extremal Optimization for protein folding simulations on the lattice

✍ Scribed by Hengyun Lu; Genke Yang

Publisher
Elsevier Science
Year
2009
Tongue
English
Weight
590 KB
Volume
57
Category
Article
ISSN
0898-1221

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✦ Synopsis

This paper presents a novel guided search strategy Extremal Optimization (EO) with constrained structure for protein folding. In the proposed algorithm, evaluating the fitness of each monomer in an amino-acid sequence is introduced to guide the improvement of the conformation. In addition, a constrained structure is proposed to reduce the complexity of algorithm. We demonstrate that EO can be applied successfully to the protein folding problem. The results show that the algorithm can find the best solutions so far for the listed benchmarks. Within the achieved results, the search converged rapidly and efficiently.

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## Abstract A three‐dimensional lattice model of protein designed to assimilate lysozyme is introduced. An attractive interaction is assumed to work between preassigned specific pairs of units, when they occupy the nearest‐nighbor lattice points. The behavior of this lattice lysozyme is studied by