Reviewed Papers

2009

• Tadaomi Furuta, Kentaro Shimizu, Tohru Terada (2009). "Accurate prediction of native tertiary structure of protein using molecular dynamics simulation with the aid of the knowledge of secondary structures" Chemical Physics Letters, 472, 134-139.

2008

• Hiromasa Uchimura, Tadafumi Horisaki, Takashi Umeda, Haruko Noguchi, Yusuke Usami, Li Li, Tohru Terada, Shugo Nakamura, Kentaro Shimizu, Tetsuo Takemura, Hiroshi Habe, Kazuo Furihata, Toshio Omori, Hisakazu Yamane, and Hideaki Nojiri (2008). "Alteration of the Substrate Specificity of the Angular Dioxygenase Carbazole 1,9a-Dioxygenase" Bioscience, Biotechnology, and Biochemistry, 72, 3237-3248.
• Tohru Terada, Daisuke Satoh, Tsutomu Mikawa, Yutaka Ito, Kentaro Shimizu (2008). "Understanding the roles of amino acid residues in tertiary structure formation of chignolin by using molecular dynamics simulation" Proteins: Structure, Function, and Bioinformatics, 73, 621-631.
• Tohru Terada and Kentaro Shimizu (2008). "A comparison of generalized Born methods in folding simulations" Chemical Physics Letters, 460, 295-299.
• Akiko Shimizu-Ibuka, Yuji Nakai, Keisuke Nakamori, Yuji Morita, Ken-ichiro Nakajima, Koji Kadota, Hirohito Watanabe, Satoshi Okubo, Tohru Terada, Tomiko Asakura, Takumi Misaka, and Keiko Abe (2008). "Biochemical and Genomic Analysis of Neoculin Compared to Monocot Mannose-Binding Lectins" Journal of Agricultural and Food Chemistry, 56, 5338-5344.
• Ken-ichiro Nakajima, Yuji Morita, Ayako Koizumi, Tomiko Asakura, Tohru Terada, Keisuke Ito, Akiko Shimizu-Ibuka, Jun-ichi Maruyama, Katsuhiko Kitamoto, Takumi Misaka, and Keiko Abe (2008). "Acid-induced sweetness of neoculin is ascribed to its pH-dependent agonistic-antagonistic interaction with human sweet taste receptor" The FASEB Journal, 22, 2323-2330.
• Ryuichiro Ishitani, Tohru Terada, Kentaro Shimizu (2008). "Refinement of comparative models of protein structure by using multicanonical molecular dynamics simulations" Molecular Simulation, 34, 327-336.

2007

• Keisuke Ito, Tomiko Asakura, Yuji Morita, Ken-ichiro Nakajima, Ayako Koizumi, Akiko Shimizu-Ibuka, Katsuyoshi Masuda, Masaji Ishiguro, Tohru Terada, Jun-ichi Maruyama, Katsuhiko Kitamoto, Takumi Misaka, and Keiko Abe (2007). "Microbial production of sensory-active miraculin" Biochemical and Biophysical Research Communications, 360, 407-411.
• Satoshi Yamasaki, Shugo Nakamura, Tohru Terada, and Kentaro Shimizu (2007). "Mechanism of the Difference in the Binding Affinity of E. coli tRNA^Gln to Glutaminyl-tRNA Synthetase Caused by Noninterface Nucleotides in Variable Loop" Biophysical Journal, 92, 192-200.

2006

• Ryota Jono, Kentaro Shimizu, and Tohru Terada (2006). "A multicanonical ab initio molecular dynamics method: Application to conformation sampling of alanine tripeptide" Chemical Physics Letters, 432, 306-312.
• Wei Cao, Kazuya Sumikoshi, Tohru Terada, Shugo Nakamura, and Kentaro Shimizu (2006). "Insight of the Signal Motif of GPI-(like)-anchored Proteins by using SVM" Proceedings of 2006 International Conference on Bioinformatics & Computational Biology, Editors: Hamid R. Arabnia and Homayoun Valafar, Las Vegas, USA, 541-546.
• Koji Kadota, Jiazhen Ye, Yuji Nakai, Tohru Terada, and Kentaro Shimizu (2006). "ROKU: a novel method for identification of tissue-specific genes" BMC Bioinformatics, 7, 294.
• Ryuichiro Ishitani, Kentaro Shimizu, and Tohru Terada (2006). "Evaluation of efficiency of reference potential spatial warping algorithm in conformational sampling of peptides" Journal of Chemical Physics, 124, 214902.
• Daisuke Satoh, Kentaro Shimizu, Shugo Nakamura, Tohru Terada (2006). "Folding free-energy landscape of a 10-residue mini-protein, chignolin" FEBS Letters, 580, 3422-3426.
• Akiko Shimizu-Ibuka, Yuji Morita, Tohru Terada, Tomiko Asakura, Ken-ichiro Nakajima, So Iwata, Takumi Misaka, Hiroyuki Sorimachi, Soichi Arai, and Keiko Abe (2006). "Crystal Structure of Neoculin: Insights into its Sweetness and Taste-modifying Activity" Journal of Molecular Biology, 359, 148-158.

2005

• Kazuya Sumikoshi, Tohru Terada, Shugo Nakamura, Kentaro Shimizu (2005). "A Fast Protein-Protein Docking Algorithm Using Series Expansion in Terms of Spherical Basis Functions" Genome Informatics, 16(2), 161-173.
• Hideaki Nojiri, Yuji Ashikawa, Haruko Noguchi, Jeong-Won Nam, Masaaki Urata, Zui Fujimoto, Hiromasa Uchimura, Tohru Terada, Shugo Nakamura, Kentaro Shimizu, Takako Yoshida, Hiroshi Habe, and Toshio Omori (2005). "Structure of the Terminal Oxygenase Component of Angular Dioxygenase, Carbazole 1,9a-Dioxygenase" Journal of Molecular Biology, 351, 355-370.
• Kazuhiko Arima, Kazuo Sato, Go Tanaka, Sachiko Kanaji, Tohru Terada, Eijiro Honjo, Ryota Kuroki, Yo Matsuo, and Kenji Izuhara (2005). "Characterization of the Interaction between Interleukin-13 and Interleukin-13 Receptors" Journal of Biological Chemistry, 280, 24915-24922.
• Xuesong Dong, Shinya Fushinobu, Eriko Fukuda, Tohru Terada, Shugo Nakamura, Kentaro Shimizu, Hideaki Nojiri, Toshio Omori, Hirofumi Shoun, and Takayoshi Wakagi (2005). "Crystal Structure of the Terminal Oxygenase Component of Cumene Dioxygenase from Pseudomonas fluorescens IP01" Journal of Bacteriology, 187, 2483-2490.

2004

• Akira Nomoto, Wataru Kaneko, Tohru Terada, Shugo Nakamura, and Kentaro Shimizu (2004). "Programming Environment Based on Distributed Shared Arrays for High-Performance Scientific Computing" Proceedings of the 2004 Symposium on Applications and the Internet-Workshops (SAINT 2004 Workshops), 630-636.
• Takanori Ishizuka, Tohru Terada, Shugo Nakamura, and Kentaro Shimizu (2004). "Improvement of accuracy of free-energy landscapes of peptides calculated with generalized Born model by using numerical solutions of Poisson's equation" Chemical Physics Letters, 393, 546-551.

2003

• Takashi Ishida, Takeshi Nishimura, Makoto Nozaki, Tsuyoshi Inoue, Tohru Terada, Shugo Nakamura, and Kentaro Shimizu (2003). "Development of an ab initio protein structure prediction system ABLE" Genome Informatics, 14, 228-237.
• Tohru Terada, Yo Matsuo, and Akinori Kidera (2003). "A method for evaluating multicanonical potential function without iterative refinement: Application to conformational sampling of a globular protein in water" Journal of Chemical Physics, 118, 4306-4311.
• Takafumi Uchida, Mari Takamiya, Morito Takahashi, Hitoshi Miyashita, Hisafumi Ikeda, Tohru Terada, Yo Matsuo, Mikako Shirouzu, Shigeyuki Yokoyama, Fumihiro Fujimori, and Tony Hunter (2003). "Pin1 and Par14 Peptidyl Prolyl Isomerase Inhibitors Block Cell Proliferation" Chemistry & Biology, 10, 15-24.

2002

• Tohru Terada and Akinori Kidera (2002). "Generalized form of the conserved quantity in constant-temperature molecular dynamics" Journal of Chemical Physics, 116, 33-41.

1996-2001 (Experimental studies)

• Tohru Terada, Mikako Shirouzu, Yasuhiro Fukumori, Fumihiro Fujimori, Yutaka Ito, Takanori Kigawa, Shigeyuki Yokoyama, and Takafumi Uchida (2001). "Solution Structure of the Human Parvulin-like Peptidyl Prolyl cis/trans Isomerase, hPar14" Journal of Molecular Biology, 305, 917-926.
• Tohru Terada, Yutaka Ito, Mikako Shirouzu, Masaru Tateno, Kyoko Hashimoto, Takanori Kigawa, Toshikazu Ebisuzaki, Koji Takio, Takehiko Shibata, Shigeyuki Yokoyama, Brian O. Smith, Ernest D. Laue, and Jonathan A. Cooper (1999). "Nuclear Magnetic Resonance and Molecular Dynamics Studies on the Interactions of the Ras-binding Domain of Raf-1 with Wild-type and Mutant Ras Proteins" Journal of Molecular Biology, 286, 219-232.
• Takashi Yabuki, Takanori Kigawa, Naoshi Dohmae, Koji Takio, Tohru Terada, Yutaka Ito, Ernest D. Laue, Jonathan A. Cooper, Masatsune Kainosho, Shigeyuki Yokoyama (1998). "Dual amino acid-selective and site-directed stable-isotope labeling of the human c-Ha-Ras protein by cell-free synthesis" Journal of Biolomecular NMR, 11, 295-306.
• Hideki Aihara, Yutaka Ito, Hitoshi Kurumizaka, Tohru Terada, Shigeyuki Yokoyama, and Takehiko Shibata (1997). "An Interaction between a Specific Surface of the C-terminal Domain of RecA Protein and Double-stranded DNA for Homologous Pairing" Journal of Molecular Biology, 274, 213-221.
• Yutaka Ito, Kazuhiko Yamasaki, Junji Iwahara, Tohru Terada, Akihide Kamiya, Mikako Shirouzu, Yutaka Muto, Gota Kawai, Shigeyuki Yokoyama, Ernest D. Laue, Markus Waelchli, Takehiko Shibata, Susumu Nishimura, and Tatsuo Miyazawa (1997). "Regional Polysterism in the GTP-Bound Form of the Human c-Ha-Ras Protein" Biochemistry, 36, 9109-9119.
• Satoko Akashi, Mikako Shirouzu, Tohru Terada, Yutaka Ito, Shigeyuki Yokoyama, and Koji Takio (1997). "Characterization of the Structural Difference between Active and Inactive Forms of the Ras Protein by Chemical Modification Followed by Mass Spectrometric Peptide mapping" Analytical Biochemistry, 248, 15-25.
• Brian O. Smith, Yutaka Ito, Andrew Raine, Sarah Teichmann, Liat Ben-Tovim, Daniel Nietlispach, R. William Broadhurst, Tohru Terada, Mark Kelly, Hartmut Oschkinat, Takehiko Shibata, Shigeyuki Yokoyama, and Ernest D. Laue (1996). "An approach to global fold determination using limited NMR data from larger proteins selectively protonated at specific residue types" Journal of Biomolecular NMR, 8, 360-368.