DFS Based Partial Pathways in GA for Protein Structure Prediction

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Title DFS Based Partial Pathways in GA for Protein Structure Prediction
Author Hoque, Md Tamjidul; Chetty, Madhu; Lewis, Andrew; Sattar, Abdul
Publication Title Pattern Recognition in Bioinformatics
Editor Madhu Chetty, Alioune Ngom, and Shandar Ahmad
Year Published 2008
Place of publication Berlin
Publisher Springer
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.
Peer Reviewed Yes
Published Yes
Publisher URI http://www.infotech.monash.edu.au/about/news/conferences/prib08/
Alternative URI http://dx.doi.org/10.1007/978-3-540-88436-1_4
Copyright Statement Copyright 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.
ISBN 978-3-540-88434-7
Conference name Third IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2008)
Location Melbourne, Australia
Date From 2008-10-15
Date To 2008-10-17
URI http://hdl.handle.net/10072/23639
Date Accessioned 2009-02-04
Language en_AU
Research Centre Institute for Integrated and Intelligent Systems
Faculty Faculty of Science, Environment, Engineering and Technology
Subject Medical Biochemistry: Proteins and Peptides (incl Medical Proteomics); Numerical Computation
Publication Type Conference Publications (Full Written Paper - Refereed)
Publication Type Code e1

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