Search Strategies in Structural Bioinformatics

Mark Oakley, Daniel Barthel, Yuri Bykov, Jonathan Garibaldi, Edmund Burke, Natalio Krasnogor, Jonathan Hirst
2008 Current protein and peptide science  
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
more » ... f 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.
doi:10.2174/138920308784534032 pmid:18537681 fatcat:2tptsm5v2recdmlorrt5c7i7k4