title: A genetic algorithm based molecular modeling technique for RNA stem-loop structures.
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.
authors.affiliation: Institute for Chemical Research, Kyoto University, Japan.
authors.forename: H
authors.initials: H
authors.lastname: Ogata
authors.forename: Y
authors.initials: Y
authors.lastname: Akiyama
authors.forename: M
authors.initials: M
authors.lastname: Kanehisa
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012360:RNA, Transfer, Phe / Q000737:chemistry
chemical_list: D012360:RNA, Transfer, Phe; D012313:RNA