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    block this user Yuri Bykov Trusted member

    Research Fellow / yxb@cs.nott.ac.uk

    School of Computer Science, University of Nottingham, Nottingham, UK

    Search strategies in structural bioinformatics.

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    Optimisation problems pervade structural bioinformatics. In this review, we describe recent work addressing a selection of bioinformatics challenges. We begin with a discussion of research into protein structure comparison, and highlight the utility of Kolmogorov complexity as a measure of structural similarity. We then turn to research into de novo protein structure prediction, in which structures are generated from first principles. In this endeavour, there is a compromise between the detail of the model and the extent to which the conformational space of the protein can be sampled. We discuss some developments in this area, including off-lattice structure prediction using the great deluge algorithm. One strategy to reduce the size of the search space is to restrict the protein chain to sites on a regular lattice. In this context, we highlight the use of memetic algorithms, which combine genetic algorithms with local optimisation, to the study of simple protein models on the two-dimensional square lattice and the face-centred cubic lattice.

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    Description

    Title : Search strategies in structural bioinformatics.
    Author(s) : Mark T Oakley, Daniel Barthel, Yuri Bykov, Jonathan M Garibaldi, Edmund K Burke, Natalio Krasnogor, Jonathan D Hirst
    Abstract : Optimisation problems pervade structural bioinformatics. In this review, we describe recent work addressing a selection of bioinformatics challenges. We begin with a discussion of research into protein structure comparison, and highlight the utility of Kolmogorov complexity as a measure of structural similarity. We then turn to research into de novo protein structure prediction, in which structures are generated from first principles. In this endeavour, there is a compromise between the detail of the model and the extent to which the conformational space of the protein can be sampled. We discuss some developments in this area, including off-lattice structure prediction using the great deluge algorithm. One strategy to reduce the size of the search space is to restrict the protein chain to sites on a regular lattice. In this context, we highlight the use of memetic algorithms, which combine genetic algorithms with local optimisation, to the study of simple protein models on the two-dimensional square lattice and the face-centred cubic lattice.
    Keywords : algorithms, computational biology, computer simulation, protein conformation, protein folding, protein structure, secondary, proteins, proteins chemistry

    Subject : unspecified
    Area : Other
    Language : English
    Year : 2008

    Affiliations School of Computer Science, University of Nottingham, Nottingham, UK
    Journal : Current protein peptide science
    Volume : 9
    Issue : 3
    Publisher : Bentham Science Publishers
    Pages : 260-274
    Url : http://www.ncbi.nlm.nih.gov/pubmed/18537681

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