Prospects for tertiary structure prediction of RNA based on secondary structure information.

Satoshi Yamasaki, Shugo Nakamura, Kazuhiko Fukui

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

Journal of chemical information and modeling 2012 Feb 27

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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.

Citation

Satoshi Yamasaki, Shugo Nakamura, Kazuhiko Fukui. Prospects for tertiary structure prediction of RNA based on secondary structure information. Journal of chemical information and modeling. 2012 Feb 27;52(2):557-67