个人简介

Academic Degrees: March 1975, the Bachelor of Science, Physics, at Department of Physics, Faculty of Science, University of Tokyo, Tokyo. 　 March 1980, the Doctor of Science, at Department of Physics, Faculty of Science, University of Tokyo, Tokyo, supervised by Prof. Dr. Akiyoshi Wada. The title of the doctor thesis is 'Dielectric studies of the biological polyelectrolytes by Fourier-synthesized-pseudorandom-noise-dielectric spectrometer'. 　 Research Experience: April 1980-July 1987, Research Associate, at Department of Applied Physics (with Prof. Dr. Koji Okano), Faculty of Engineering, University of Tokyo, Tokyo. 　 July 1985 - December 1985, Visiting Researcher, at the Astbury Department of Biophysics, Leeds University, Leeds, U.K., studying molecular graphics in the laboratory of Prof. Dr. A. C. T. North by a SERC grant of U.K. 　 August 1987 - March 1996, Director of Second Department, Protein Engineering Research Institute, Osaka, studying molecular modelling, design and analysis. 　 November 1994, Guest Professor, Institut fur Organ. Chemie und Biochemie (Prof. Dr. Georg E. Schulz), Albert-Ludwigs-University Freiburg. 　 April 1995 - March 1999, Guest Professor, Faculty of Medicine, Osaka University. 　 April 1995 - March 1999, Guest Professor, Faculty of Medicine, Kyoto University. 　 April 1996 - March 1999, Research Director, Department of Bioinformatics, Biomolecular Engineering Research Institute, Osaka. 　 April 1999 -, Professor, Laboratory of Protein Informatics, Research Center for Structural Biology, Institute for Protein Research, Osaka University. April 2012- March 2014, Advisor to Osaka University Trustees. April 2014- , Director of Institute for Protein Research, Osaka University.

研究领域

Biophysics / Protein Science / Structural Bioinformatics

Our laboratory, Laboratory of Protein Informatics, is engaged in the protein informatics researches by developing the international protein structural databases and the structural bioinformatics covering molecular modeling and design. We also perform large scale simulation calculations by parallel computers to examine free energy landscapes and biochemical functions of biomolecular systems with molecular dynamics and quantum chemistry simulations. Protein structure determination by X-ray crystallography is also our aim to understand the structure-function relationships. Research Activities Laboratory of Protein Informatics are engaged in the following protein informatics researches: Development and maintenance of international protein structural databases (PDBj) and structural bioinformatics covering molecular modeling and design. Development of new databases and Web services: eF-site, for protein surface geometry with the physicochemical properties; PreDs, for prediction of the putative double-stranded DNA binding sites of proteins based on the protein molecular surface features; and HINT, Homologous Interaction Database. Structural bioinformatics studies, focusing on protein-protein interactions. Large scale simulation calculations by parallel computers to examine free energy landscapes of biomolecular systems with the hybrid QM (Quantum mechanics) / MM (Molecular mechanics) method for analysis of biochemical reactions. Protein structure determination by X-ray crystallography and protein function analysis.

近期论文

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"Nishikawa Y., Oyama T., Kamiya N., Kon T., Toyoshima Y. Y., Nakamura H., Kurisu G., Structure of the entire stalk region of the dynein motor domain. J. Mol. Biol., accepted on June 24. 2014. Kawabata T., Nakamura H., 3D flexible alignment using 2D maximum common substructure: dependence of prediction accuracy on target-reference chemical similarity. J. Chem. Info. Model., accepted on June 4, 2014. Shirai H., Ikeda K., Yamashita K., Tsuchiya Y., Sarmiento J., Liang S., Morokata T., Mizuguchi K., Higo J., Standley D. M., Nakamura H., High-resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations. PROTEINS, accepted on April 12 2014. DOI: 10.1002/prot.24591 Fukuda I., Kamiya N., Nakamura H., The Zero-multipole summation method for estimating electrostatic interactions in molecular dynamics: analysis of the accuracy and application to liquid systems. Journal of Chemical Physics, 140, 194307, 2014. DOI: 10.1063/1.4875693 Lensink M. F., Moal I. H., Bates P. A., Kastritis P. L. Melquiond A. S. J., Karaca E., Schmitz C., van Dijk M., Bonvin A. M. J. J., Eisenstein M., Jiménez-García B., Grosdidier S., Solernou A., Pérez-Cano L., Pallara C., Fernández-Recio J., Xu J., Muthu P., Kilambi K. P., Gray J. J., Grudinin S., Derevyanko G., Mitchell J. C., Wieting J., Kanamori E., Tsuchiya Y., Murakami Y., Sarmiento J.,, Standley D. M., Shirota M., Kinoshita K., Nakamura H., Chavent M., Ritchie D. W., Park H., Ko J., Lee H., Seok C., Shen Y., Kozakov D., Vajda S., Kundrotas P. J., Vakser I. A., Pierce B. G., Hwang H., Vreven T., Weng Z., Buch I., Farkash E., Wolfson H. J., Zacharias M., Qin S., Zhou H.-Z., Huang S.-Y., Zou X., Wojdyla J. A., Kleanthous C., Wodak S. J., Blind prediction of interfacial water positions in CAPRI. PROTEINS 82, 620-632, 2014. DOI: 10.1002/prot.24439 Dasgupta B., Nakamura H., Kinjo A. R., Rigid-body motions of interacting proteins dominate multi-specific binding of Ubiquitin in a shape-dependent manner. PROTEINS 82, 77-89, 2014. DOI: 10.1002/prot.24371 Kita M., Nakamura H., Takano Y., Density functional study of the phosphate diester hydrolysis of RNA in RNA/DNA hibrid by RNase HI. Molecular Physics 112, 355-364, 2014. DOI:10.1080/00268976.2013.820854 Mashimo T., Fukunishi Y., Kamiya N., Takano Y., Fukuda I., Nakamura H., Molecular dynamics simulations accelerated by GPU for biological macromolecules with a non-Ewald scheme for electrostatic interactions. J. Chem. Theory Comput. 9, 5599-5609, 2013. DOI: 10.1021/ct400342e Moretti R., Fleishman S. J., Agius R., Torchala M., Bates P. A., Kastritis P. L., Rodrigues J. P. G. K. M., Trellet M., Bonvin A. M. J. J., Cui M., Rooman M., Gillis D., Dehouck Y., Moal I., Romero-Durana M., Perez-Cano L., Pallara C., Jimenez B., Fernandez-Recio J., Flores S., Pacella M., Kilambi K. P., Gray J. J., Popov P., Grudinin S., Esquivel-Rodríguez J., Kihara D., Zhao N., Korkin D., Zhu X., Demerdash O. N. A., Mitchell J. C., Kanamori E., Tsuchiya Y., Nakamura H., Lee H., Park H., Seok C., Sarmiento J., Liang S., Teraguchi S., Standley D. M., Shimoyama H., Terashi G., Takeda-Shitaka M., Iwadate M., Umeyama U., Beglov D., Hall D. R., Kozakov D., Vajda S., Pierce B. G., Hwang H., Vreven T., Weng Z., Huang Y., Li H., Yang X., Ji X., Liu S., Xiao Y., Zacharias M., Qin S., Zhou H.-X., Huang S.-Y., Zou X., Velankar S., Janin J., Wodak S. J., Baker D., Community-wide evaluation of methods forpredicting the effect of mutations on protein–protein interactions. PROTEINS 81, 1980-1987, 2013. Arakawa T., Kamiya N., Nakamura H., Fukuda I., Molecular dynamics simulations of a double-stranded DNA in an explicit solvent model with zero-dipole summation method. PLoS One 8, e76606, 2013. Murakami Y., Kinoshita K., Kinjo A. R., Nakamura H., Exhaustive comparison and classification of ligand-binding surfaces in proteins. Protein Science 22, 1379-1391, 2013. Sato J., Kozaki K., Handa S., Ikeda T., Saka R., Tomizuka K., Nishiyama Y., Okumura T., Hirai S., Ohno T., Ohta M., Date S., Nakamura H., Protein Experimental Information Management System (PREIMS) Based on Ontology: Development and Applications. IPSJ Trans. Bioinfo. 6, 9–17, 2013. Higo J., Umezawa K., Nakamura H., A virtual-system coupled multicanonical molecular dynamics simulation: Principles and applications to free-energy landscape of protein–protein interaction with an all-atom model in explicit solvent. J. Chem. Phys. 138, 184106, 2013. Fukunishi Y., Nakamura H., Improved estimation of protein-ligand binding free energy by using ligand-entropy and mobility of water molecules. Pharmaceuticals 6, 604-622, 2013. Kamioka T., Sohya S., Wu N., Maki T., Matsuda T., Ikegami T., Nakamura H., Kuroda Y., Extraction of Recombinant Protein from Escherichia coli by Using a Novel Cell Autolysis Activity of VanX. Analytical Biochemistry 439, 212-217, 2013. Kamiya N., Fukuda I., Nakamura H., Application of zero-dipole summation method to molecular dynamics simulations of amembrane protein system. Chem. Phys. Lett. 568-569, 26-32, 2013 (Editor's Choice). Ueda K., Yamanaka S., Nakata K., Ehara M., Okumura M., Yamaguchi K., Nakamura H., Linear Response Function Approach for the Boundary Problem of QM/MM Methods. Int. J. Quant. Chem. 113, 336-341, 2013. Berman H. M., Kleywegt G. J., Nakamura H., Markley J. L., How community has shaped the Protein Data Bank. Structure 21, 1485-1491, 2013. Hagiwara Y., Ohno K., Kamohara M., Takasaki J., Watanabe T., Fukunishi Y., Nakamura H., Orita M., Molecular modeling of vasopressin receptor and in silico screening of V1b receptor antagonists. Expert Opin Drug Discov. 8, 951-964, 2013. Dasgupta B., Nakamura H., Kinjo A. R., Counterbalance of ligand- and self-coupled motions characterizes multispecificity of ubiquitin. Protein Science 22, 168–178, 2012.