A Computer Modeling Method for the Three-dimensional Structure of RNA

Hiroyuki Ogata (ogata@kuicr.kyoto-u.ac.jp)
Yutaka Akiyama (akiyama@kuicr.kyoto-u.ac.jp)
Minoru Kanehisa (kanehisa@kuicr.kyoto-u.ac.jp)

Institute for Chemical Research
Kyoto University
Uji, Kyoto 611


We are developing a computational method for automatically organizing collections of structural knowledge of RNA into a three-dimensional (3-D) form. The goal of our method for modeling of RNA structure is to find, as much as possible, conformations of RNA which satisfy the constraints from experiments and sequence analysis and, at the same time, whose local conformations are close to some representative conformations. For efficient conformational search, we used a genetic algorithm as a trial. We applyed our method in modeling a single stranded region of an RNA for the estimation of efficiency of our method.