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. 1995 Feb 11;23(3):419–426. doi: 10.1093/nar/23.3.419

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

H Ogata 1, Y Akiyama 1, M Kanehisa 1
PMCID: PMC306692  PMID: 7533901

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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Selected References

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