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バイオインフォマティクス推進センター事業(BIRD) 第8回研究開発成果報告会 知識発見への挑戦 〜バイオインフォマティクスの飛躍に向けて〜 要旨集  16-21
高精度タンパク質間相互作用予測システムの開発
清水 謙多郎


[1] O. Hirose, K. Shimizu: A self-organizing state space approach to infer time-varying causalities between regulatory proteins. Proceedings of International Conference on Information Technology in Bio- and Medical Informatics, Lecture Notes in Computer Science, 6266, 158-171 (2010).
[2] S. Someya, M. Kakuta, M. Morita, K. Sumikoshi, W. Cao, Z. Ge, O. Hirose, S. Nakamura, T. Terada, K. Shimizu: Prediction of carbohydrate-binding proteins from sequences using support vector machines. Advances in Bioinformatics, 2010, 289301 (2010).
[3] M. Morita, S. Nakamura, K. Shimizu: Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures. PROTEINS: Structure, Function, and Bioinformatics, 73, 2, 468-479 (2008).
[4] M. Morita, T. Terada, S. Nakamura, K. Shimizu: BUDDY-system: A web site for constructing a dataset of protein pairs between ligand-bound and unbound states. BMC Research Notes, 4, 143 (2011).
[5] K. Sumikoshi, T. Terada, S. Nakamura, K. Shimizu: Protein-Protein Docking Using Multi-layered Spherical Basis Functions. Proceedings of the 2011 International Conference on Bioscience, Biochemistry and Bioinformatics, 342-347 (2011).
[6] R. Jono, Y. Watanabe, K. Shimizu, T. Terada: Multicanonical ab inito QM/MM Molecular Dynamics Simulation of a Peptide in an Aqueous Environment, J. Comput. Chem., 31, 6, 1168-1175 (2009).
[7] K. Urano, T. Daimon, Y. Banno, K. Mita, T. Terada, K. Shimizu, S. Katsuma, T. Shimada: Molecular defect of isovaleryl-CoA dehydrogenase in the skunk mutant of silkworm, Bombyx mori. FEBS Journal, 277, 4452-4463 (2010).
[8] H. Nojiri, Structural and molecular genetic analyses of the bacterial carbazole degradation system. Biosci. Biotechnol. Biochem., in press.
[9] K. Inoue, Y. Ashikawa, T. Umeda, M. Abo, J. Katsuki, Y. Usami, H. Noguchi, Z. Fujimoto, T. Terada, H. Yamane, H. Nojiri: Specific interactions between the ferredoxin and terminal oxygenase components of a class IIB Rieske nonheme iron oxygenase, carbazole 1,9a-dioxygenase. Journal of Molecular Biology, 392, 436-451 (2009).
[10] T. Umeda, J. Katsuki, Y. Ashikawa, Y. Usami, K. Inoue, H. Noguchi, Z. Fujimoto, H. Yamane, H. Nojiri: Crystallization and preliminary X-ray diffraction studies of a terminal oxygenase of carbazole 1,9a-dioxygenase from Novosphingobium sp. KA1. Acta Cryst., F66, 1480-1483 (2010).