README RNA_Structure_Prediction-K (Linux) 1. KNIME package (32bit or 64bit) References: ToGo-Workflow: Yamasaki S, Amemiya T, Yabuki Y, Horimoto K, Fukui K, "ToGo-WF: prediction of RNA tertiary structures and RNA-RNA/protein interactions using the KNIME workflow." J. Computer-Aided Molecular Design 33: 497-507 (2019) RASSIE: S. Yamasaki, S. Nakamura, K. Fukui, "Prospects for tertiary structure prediction of RNA based on secondary structure information." Journal of Chemical Information and Modeling, 52, 557-567 (2012) RASCAL: S. Yamasaki, T. Hirokawa, K. Asai, K. Fukui, "Tertiary structure prediction of RNA-RNA complexes using secondary structure and fragment based method." Journal of Chemical Information and Modeling, 54(2) pp. 672-682 (2014). IPknot: Kengo Sato, Yuki Kato, Michiaki Hamada, Tatsuya Akutsu and Kiyoshi Asai, "IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming", Bioinformatics, vol. 27, no. 13, pp. i85-i93, Jul. 2011 http://rtips.dna.bio.keio.ac.jp/ipknot/ RactIP: Yuki Kato, Kengo Sato, Michiaki Hamada, Yoshihide Watanabe, Kiyoshi Asai and Tatsuya Akutsu, "RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming", Bioinformatics, vol. 26, no. 18, pp. i460-i466, Sep. 2010 http://rtips.dna.bio.keio.ac.jp/ractip/