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Evolutionary decision rules for predicting protein contact maps. (English) Zbl 1328.92054

Summary: Protein structure prediction is currently one of the main open challenges in Bioinformatics. The protein contact map is an useful, and commonly used, representation for protein 3D structure and represents binary proximities (contact or non-contact) between each pair of amino acids of a protein. In this work, we propose a multiobjective evolutionary approach for contact map prediction based on physico-chemical properties of amino acids. The evolutionary algorithm produces a set of decision rules that identifies contacts between amino acids. The rules obtained by the algorithm impose a set of conditions based on amino acid properties to predict contacts. We present results obtained by our approach on four different protein data sets. A statistical study was also performed to extract valid conclusions from the set of prediction rules generated by our algorithm. Results obtained confirm the validity of our proposal.

MSC:

92D20 Protein sequences, DNA sequences
92D15 Problems related to evolution
92C40 Biochemistry, molecular biology
90C90 Applications of mathematical programming
90C59 Approximation methods and heuristics in mathematical programming
90C29 Multi-objective and goal programming
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