Nucleic Acid Res. 23, 152-154 (1996)
A genetic algorithm based molecular modeling technique for
RNA stem-loop structures
Hiroyuki Ogata, Yutaka Akiyama and Minoru Kanehisa*
Institute for Chemical Research, Kyoto University
Uji, Kyoto 611, Japan
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.
* Corresponding author:
Minoru Kanehisa
Institute for Chemical Research, Kyoto University
Uji, Kyoto 611, Japan
Fax: +81-774-32-8235
E-mail: kanehisa@kuicr.kyoto-u.ac.jp