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Erschienen in:
2014 | OriginalPaper | Buchkapitel
Constraint-Based Evolutionary Local Search for Protein Structures with Secondary Motifs
verfasst von : Swakkhar Shatabda, M. A. Hakim Newton, Abdul Sattar
Erschienen in: PRICAI 2014: Trends in Artificial Intelligence
Verlag: Springer International Publishing
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On-lattice protein structure prediction with empirical energy minimisation has drawn significant research effort. However, energy minimisation with free-modelling not necessarily leads to structures that are similar to the native structure of the given protein. In this paper, we show that energy minimisation has a positive correlation with structural similarity measures if we consider secondary motifs. We then present a constraint-based evolutionary local search framework for on-lattice protein structure prediction using secondary structural information. We approximate secondary motifs such as
α
-helix and
β
-strands on the lattice and propose a set of neighbourhood generation operators that respect those motifs. Our experimental results show significant improvement over the state-of-the-art methods in terms of similarity with the native structures determined by laboratory methods.