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Current Protein & Peptide Science

Volume 9 Issue 3
ISSN: 1389-2037
eISSN: 1875-5550

 

   All Titles

  Search Strategies in Structural Bioinformatics
  pp.260-274 (15) Authors: 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.

 
  Affiliation: School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom .
 
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