title: Prospects for tertiary structure prediction of RNA based on secondary structure information.
abstract: We developed a method, called RNA Assembler using Secondary Structure Information Effectively (RASSIE), for predicting RNA tertiary structures using known secondary structure information. We attempted a fragment assembly-based method that uses a secondary structure-based fragment library. For several typical target structures such as stem-loops, bulge-loops, and 2-way junctions, our method provided numerous good quality candidate structures in less computational time than previously proposed methods. By using a high-resolution potential energy function, we were able to select good predicted structures from candidate structures. This method of efficient conformational search and detailed structure evaluation using high-resolution potential is potentially useful for the tertiary structure prediction of RNA.
authors.affiliation: Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan. s.yamasaki@aist.go.jp
authors.forename: Satoshi
authors.initials: S
authors.lastname: Yamasaki
authors.forename: Shugo
authors.initials: S
authors.lastname: Nakamura
authors.forename: Kazuhiko
authors.initials: K
authors.lastname: Fukui
mesh_terms: D000465:Algorithms; D008722:Methods; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*
chemical_list: D012313:RNA