Please use this identifier to cite or link to this item: http://hdl.handle.net/1893/15821
Appears in Collections:Computing Science and Mathematics Journal Articles
Peer Review Status: Refereed
Title: Search strategies in structural bioinformatics
Authors: Oakley, Mark T
Barthel, Daniel
Bykov, Yuri
Garibaldi, Jonathan M
Burke, Edmund
Krasnogor, Natalio
Hirst, Jonathan D
Contact Email: e.k.burke@stir.ac.uk
Issue Date: 2008
Publisher: Bentham Science
Citation: Oakley MT, Barthel D, Bykov Y, Garibaldi JM, Burke E, Krasnogor N & Hirst JD (2008) Search strategies in structural bioinformatics, Current Protein and Peptide Science, 9 (3), pp. 260-274.
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.
Type: Journal Article
URI: http://hdl.handle.net/1893/15821
DOI Link: http://dx.doi.org/10.2174/138920308784534032
Rights: The publisher does not allow this work to be made publicly available in this Repository. Please use the Request a Copy feature at the foot of the Repository record to request a copy directly from the author. You can only request a copy if you wish to use this work for your own research or private study.
Affiliation: University of Nottingham
University of Nottingham
Computing Science - CSM Dept
University of Nottingham
Deputy Principal's Office
University of Nottingham
University of Nottingham

Files in This Item:
File Description SizeFormat 
Search strategies in structural bioinformatics.pdf355.73 kBAdobe PDFUnder Embargo until 31/12/2999     Request a copy

Note: If any of the files in this item are currently embargoed, you can request a copy directly from the author by clicking the padlock icon above. However, this facility is dependant on the depositor still being contactable at their original email address.

This item is protected by original copyright



Items in the Repository are protected by copyright, with all rights reserved, unless otherwise indicated.

If you believe that any material held in STORRE infringes copyright, please contact library@stir.ac.uk providing details and we will remove the Work from public display in STORRE and investigate your claim.