A genetic algorithm based molecular modeling technique for RNA stem-loop structures.

H Ogata; Y Akiyama; M Kanehisa

doi:10.1093/nar/23.3.419

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A genetic algorithm based molecular modeling technique for RNA stem-loop structures.

H Ogata·Y Akiyama·M Kanehisa

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Abstract

A new modeling technique for arriving at the three dimensional (3-D) structure of an RNA stem-loop has been developed based on a conformational search by a genetic algorithm and the following refinement by energy minimization. The genetic algorithm simultaneously optimizes a population of conformations in the predefined conformational space and generates 3-D models of RNA. The fitness function to be optimized by the algorithm has been defined to reflect the satisfaction of known conformational constraints. In addition to a term for distance constraints, the fitness function contains a term to constrain each local conformation near to a prepared template conformation. The technique has been applied to the two loops of tRNA, the anticodon loop and the T-loop, and has found good models with small root mean square deviations from the crystal structure. Slightly different models have also been found for the anticodon loop. The analysis of a collection of alternative models obtained has revealed statistical features of local variations at each base position.

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Algorithms Base Sequence Models, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA RNA, Transfer, Phe Journal Article Research Support, Non-U.S. Gov't

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H Ogata, Y Akiyama, M Kanehisa. 1995-02-11. A genetic algorithm based molecular modeling technique for RNA stem-loop structures.. https://doi.org/10.1093/nar%2F23.3.419

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