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  • Spiral Search: A Hydrophobic-Core Directed Local Search for Simplified PSP on 3D FCC Lattice

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    Author(s)
    Rashid, Mahmood A
    Newton, MA Hakim
    Hoque, Md Tamjidul
    Shatabda, Swakkhar
    Pham, Duc Nghia
    Sattar, Abdul
    Griffith University Author(s)
    Sattar, Abdul
    Pham, Nghia N.
    Hoque, Md T.
    Rashid, Mahmood A.
    Newton, MAHakim A.
    Shatabda, Swakkhar
    Year published
    2013
    Metadata
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    Abstract
    Background: Protein structure prediction is an important but unsolved problem in biological science. Predicted structures vary much with energy functions and structure-mapping spaces. In our simplified ab initio protein structure prediction methods, we use hydrophobic-polar (HP) energy model for structure evaluation, and 3-dimensional face-centred-cubic (FCC) lattice for structure mapping. For HP energy model, developing a compact hydrophobic-core (HC) is essential for the progress of the search. The hydrophobic-core (H-core) helps find a stable structure with the lowest possible free energy. Results: In order to build ...
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    Background: Protein structure prediction is an important but unsolved problem in biological science. Predicted structures vary much with energy functions and structure-mapping spaces. In our simplified ab initio protein structure prediction methods, we use hydrophobic-polar (HP) energy model for structure evaluation, and 3-dimensional face-centred-cubic (FCC) lattice for structure mapping. For HP energy model, developing a compact hydrophobic-core (HC) is essential for the progress of the search. The hydrophobic-core (H-core) helps find a stable structure with the lowest possible free energy. Results: In order to build H-core, we present a new Spiral Search algorithm based on tabu-guided local search. Our algorithm uses a novel H-core directed guidance heuristic that squeezes the structure around a dynamic hydrophobic-core-centre (HCC). We applied random-walk for breaking premature H-cores to avoid early convergence. We used a novel relay-restart (RR) technique to handle stagnation. Conclusions: We tested our algorithms on a set of benchmark proteins. The experimental results show that our spiral search performs better in comparison to state-of-the art local search algorithms for simplified protein structure prediction. We also experimentally show the effectiveness of the relay-restart.
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    Conference Title
    BMC BIOINFORMATICS
    Volume
    14
    Publisher URI
    Http://www.apbc2013.org/
    DOI
    https://doi.org/10.1186/1471-2105-14-S2-S16
    Copyright Statement
    © 2013 Rashid et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
    Note
    Page numbers are not for citation purposes. Instead, this article has the unique article number of S16.
    Subject
    Mathematical sciences
    Biological sciences
    Information and computing sciences
    Artificial intelligence not elsewhere classified
    Publication URI
    http://hdl.handle.net/10072/53603
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    • Conference outputs

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