DFS Based Partial Pathways in GA for Protein Structure Prediction

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Author(s)
Hoque, Md Tamjidul
Chetty, Madhu
Lewis, Andrew
Sattar, Abdul
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Chetty, M

Ngom, A

Ahmad, S

Date
2008
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591021 bytes

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application/pdf

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Melbourne, AUSTRALIA

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Abstract

Nondeterministic conformational search techniques, such as Genetic Algorithms (GAs) are promising for solving protein structure prediction (PSP) problem. The crossover operator of a GA can underpin the formation of potential conformations by exchanging and sharing potential sub-conformations, which is promising for solving PSP. However, the usual nature of an optimum PSP conformation being compact can produce many invalid conformations (by having non-self-avoiding-walk) using crossover. While a crossover-based converging conformation suffers from limited pathways, combining it with depth-first search (DFS) can partially reveal potential pathways. DFS generates random conformations increasingly quickly with increasing length of the protein sequences compared to random-move-only-based conformation generation. Random conformations are frequently applied for maintaining diversity as well as for initialization in many GA variations.

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PATTERN RECOGNITION IN BIOINFORMATICS, PROCEEDINGS

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5265

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© 2008 Springer-Verlag Berlin Heidelberg. This is the author-manuscript version of this paper. Reproduced in accordance with the copyright policy of the publisher. Please refer to the conference's website for access to the definitive, published version.

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Subject

Numerical computation and mathematical software

Medical biochemistry - proteins and peptides (incl. medical proteomics)

Information and computing sciences

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