Higo J., Kasahara K., Nakamura H., Multi-dimensional virtual system introduced to enhance canonical sampling. J. Chem. Phys. in press. accepted on 12-September-2017.


Imada Y., Nakamura H., Takano Y., Density functional study of porphyrin distortion effects on redox potential of heme. J. Comput. Chem., in press. Published on 2-September-2017. DOI: 10.1002/jcc.25058


Kinjo A.R., Bekker G.-J., Wako H., Endo S., Tsuchiya Y., Sato H., Nishi H., Kinoshita K., Suzuki H., Kawabata T., Yokochi M. Iwata T., Kobayashi N., Fujiwara T., Kurisu G., Nakamura H., New tools and functions in Data-out activities at Protein Data Bank Japan (PDBj) Protein Science, in press. accepted on 14-August-2017. DOI: 10.1002/pro.3273


Burley S.K., Kurisu G., Markley J.L., Nakamura H., Velankar S., Berman H.M., Sali A., Schwede T., Trewhella J., PDB-Dev: A Prototype System for Depositing Integrative/Hybrid Structural Models. Structure, 25 (9), 1317-1318, 2017.


Bekker G.-J., Kamiya N., Araki M., Fukuda I., Okuno Y., Nakamura H., Accurate prediction of complex structure and affinity for a flexible protein receptor and its inhibitor. J. Chem. Theory Comput. 13 (6), 2389-2399, 2017. DOI: 10.1021/acs.jctc.6b01127


Young J.Y., Westbrook J.D., Feng Z., Sala R., Peisach E., Oldfield T.J., Sen S., Gutmanas A., Armstrong D.R., Berrisford J.M., Chen L., Chen M., Costanzo L.D., Dimitropoulos D., Gao G.,  Ghosh S., Gore S., Guranovic V., Hendrickx P.M.S., Hudson B.P., Igarashi R., Ikegawa, Kobayashi N., Lawson C.L., Liang Y., Mading S., Mak L., Mir M.S., Mukhopadhyay A., Patwardhan A., Persikova I., Rinaldi L., Sanz-Garcia E., Sekharan M.R., Shao C., Swaminathan G.J., Tan L., Ulrich E.L., van Ginkel G., Yamashita R., Yang H., Zhuravleva M.A., Quesada M., Kleywegt G.J., Berman H.M., Markley J.L., Nakamura H., Velankar S., Burley S.K., OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive. Structure 25, 536-545, 2017. DOI: 10.1016/j.str.2017.01.004


Kasahara K., Shiina M., Fukuda I., Ogata K. Nakamura H., Molecular mechanisms of cooperative binding of transcription factors Runx1CBFbEts1 on the TCRa gene enhancer. PloS One 12 (2), e0172654, 2017. DOI:10.1371/journal.pone.0172654


Higo J., Kasahara K., Dasgupta B., Nakamura H., Enhancement of canonical sampling by virtual-state transitions. J. Chem. Phys. 146, 044104, 2017. DOI:


Kinjo, A.R. Bekker G.-J., Suzuki H., Tsuchiya Y., Kawabata T., Ikegawa Y., Nakamura H., Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures. Nucleic Acids Research 45 (D1) 282-288, 2017. DOI: 10.1093/nar/gkw962


Dasgupta B., Nakamura H., Higo J., Flexible binding simulation by a novel and improved version of virtual-system coupled adaptive umbrella sampling. Chem. Phys. Lett. 662, 327-332 2016. DOI: 10.1016/j.cplett.2016.09.059


Shimba N., Kamiya N., Nakamura H., Model Building of Antibody-Antigen Complex Structures Using GBSA Scores. J. Chem. Inf. Model. 56 (10), 2005-2012, 2016. DOI: 10.1021/acs.jcim.6b00066


Iida S., Mashimo T., Kurosawa T., Hojo H., Muta H., Goto Y., Fukunishi Y., Nakamura H., Higo J., Variation of Free-Energy Landscape of the p53 C-terminal Domain Induced by Acetylation: Enhanced Conformational Sampling. J. Comput. Chem. 37 (31), 2687-2700 , 2016. DOI: 10.1002/jcc.24494, dec 5


Bekker H.-J., Nakamura H., Kinjo A.R., Molmil: a molecular viewer for the PDB and beyond. J. Cheminform. 8:42, 2016.  DOI 10.1186/s13321-016-0155-1


Berman H.M., Burley S.K., Kleywegt G.J., Markley J.L., Nakamura, Velankar S., The archiving and dissemination of biological structure data. Curr Opin Struct Biol. 40, 17-22, 2016. DOI: 10.1016/


Kasahara K., Ma B., Goto K., Dasgupta B., Higo J., Fukuda I., Mashimo T., Akiyama Y., Nakamura H., myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme. Biophys. PhysicoBiol. 13, 209-216, 2016. DOI: 10.2142/biophysico.13.0_209


Nishigami H., Kamiya N., Nakamura H., Revisiting Antibody Modeling Assessment for CDR-H3 loop. Protein Engineering, Design and Selection 29 (11), 477-184, 2016. DOI: 10.1093/protein/gzw028


Kamiya N., Mashimo T., Takano Y., Kon T., Kurisu G., Nakamura H., Elastic properties of dynein motor domain obtained from all-atom molecular dynamics simulations. Protein Engineering, Design and Selection 29 (8), 317-325, 2016. DOI: 10.1093/protein/gzw022


Yokochi M., Kobayashi N., Ulrich E.L., Kinjo A.R., Iwata T., Ioannidis Y.E., Livny M., Markley J.L., Nakamura H., Kojima C., Fujiwara T., Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins. Journal of Biomedical Semantics 7:16, 2016. DOI: 10.1186/s13326-016-0057-1


Iida S., Nakamura H., Higo J., Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation. Biochemical Journal, 473 (12), 1651-1662, 2016.


Kasahara K., Mohan N., Fukuda I., Nakamura H., mDCC_tools: Characterizing Multi-modal Atomic Motions in Molecular Dynamics Trajectories. Bioinformatics 32 (16), 2531-2533, 2016. DOI: 10.1093/bioinformatics/btw129


Wang H., Nakamura H., Fukuda I., A critical appraisal of the zero-multipole method: Structural, thermodynamic, dielectrid, and dynamical properties of a water system. Journal of Chemical Physics 144 (11), 114503,, 2016. DOI: 10.1063/1.4943956


Takano Y., Nakata K., Yonezawa Y., Nakamura H., Development of Massive Multilevel Molecular Dynamics Simulation Program, Platypus (PLATform for dYnamic Protein Unified Simulation), for the Elucidation of Protein. J. Comput. Chem. 37, 1125-1132, 2016. DOI: 10.1002/jcc.24318


Takano Y., Kusaka A., Nakamura H., Density functional study of molecular interactions in secondary structures of proteins. Biophys. Physicobiol. 13, 27-35,  2016. DOI: 10.2142/biophysico.13.0_27.


Suzuki H., Kawabata T., Nakamura H., Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB. Bioinformatics, 32 (4), 619-620, 2016. DOI: 10.1093/bioinformatics/btv614


Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD, Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure 23 (7), 1156-1167, 2015. DOI: 10.1016/j.str.2015.05.013


Nguyen H., Tran T., Fukunishi Y., Higo J., Nakamura H., Le L., Computational Study of Drug Binding Affinity to Influenza A Neuraminidase Using Smooth Reaction Path Generation (SRPG) Method. Journal of Chemical Information and Modeling, 55 (9), 1936-1943, 2015. DOI: 10.1021/acs.jcim.5b00319, 


Higo J., Dasgupta B., Mashimo T., Kasahara K., Fukunishi Y., Nakamura H., Virtual-system coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking. Journal of Computational Chemistry 36 (20), 1489-1501, 2015. DOI: 10.1002/jcc.23948


Suzuki K., Mizushima H., Abe H., Iwamoto R., Nakamura H., Mekada E., Identification of diphtheria toxin R domain mutants with enhanced inhibitory activity against HB-EGF. J Biochem. 157 (5) 331-343, 2014. DOI: 10.1093/jb/mvu079


Fukunishi Y., Kurosawa T., Mikami Y., Nakamura H., Prediction of synthetic accessibility based on commercially available compound databases. J Chem Inf Model. 54 (12), 3259-3267, 2014. doi: 10.1021/ci500568d


Kasahara K., Fukuda I., Nakamura H., A Novel Approach of Dynamic Cross Correlation Analysis on Molecular Dynamics Simulations and its Application to Ets1 dimer–DNA Complex. PLoS ONE, 9 (11), e112419, 2014. DOI: 10.1371/journal.pone.0112419.


Berman H.M., Burley S.K., Kleywegt J.G., Nakamura H., Markley J.L., Response to On prompt update of literature references in the Protein Data Bank. Acta Crystallogr D Biol Crystallogr. 70(Pt 10): 2780, 2014. doi: 10.1107/S1399004714020513.


Mitsuta Y., Yamanaka S., Yamaguchi K., Okumura M., Nakamura H., Theoretical investigation on nearsightedness of finite model and molecular systems based on linear response function analysis. Molecules. 19 (9), 13358-13373, 2014. doi: 10.3390/molecules190913358.


Yamashita K., Ikeda K., Amada K., Liang S., Tsuchiya Y., Nakamura H., Shirai H., Standley D.M., Kotai Antibody Builder: Automated, high-resolution structural modeling of antibodies. Bioinformatics, 30 (22), 3279-3280, 2014, DOI: 10.1093/bioinformatics/510


Berman H.M., Kleywegt G.J., Nakamura H., Markley J.L., The Protein Data Bank archive as an open data resource. J Comput Aided Mol Des. 28(10), 1009-1014, 2014. DOI: 10.1007/s10822-014-9770-y.


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. (2014) Journal of Molecular Biology 426, 3232–3245, 2014. DOI: 10.1016/j.jmb.2014.06.023


Kawabata T., Nakamura H., 3D flexible alignment using 2D maximum common substructure: dependence of prediction accuracy on target-reference chemical similarity. Journal of Chemical Information and Modeling 54 (7), 1850-1863, 2014. DOI: 10.1021/ci500006d


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


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 82 (8) 1624-1635, 2014. DOI: 10.1002/prot.24591


Dasgupta B., Kasahara K., Kamiya K., Nakamura H., Kinjo A,.R.  Specific non-local interactions are not necessary for recovering native protein dynamics. PLoS One 9 (3), e91347, 2014. DOI: 10.1371/journal.pone.0091347


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, 2014.  DOI: 10.1021/ct400342e.


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 (4), 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, (1) 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 (3-4), 355-364,  2014. DOI:10.1080/00268976.2013.820854.


Berman H., Kleywegt G.J., Nakamura H., Markley J.L., Comment on timely deposition of macromolecular structures is necessary for peer review by Joosten et al. Acta Crystallogr D Biol Crystallogr. 69(Pt 12): 2296, 2013. doi: 10.1107/S0907444913029168.


Berman H., Kleywegt G.J., Nakamura H., Markley J.L., Comment on on the propagation of errors by Jaskolski. Acta Crystallogr D Biol Crystallogr. 69 (Pt 12): 2297, 2013. doi: 10.1107/S090744491302917X.


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.


Fukunishi Y., Nakamura H. Statistical Estimation of the Protein-Ligand Binding Free Energy Based On Direct Protein-Ligand Interaction Obtained by Molecular Dynamics Simulation. Pharmaceuticals 5, 1063-1078, 2012.


Fukuda I., Kamiya N., Yonezawa Y., Nakamura H. Simple and Accurate Scheme to Compute Electrostatic Interactions: Zero-dipole Summation Technique for Molecular System and Application to Bulk Water. J. Chem. Phys. 137, 054314, 2012.


Kinjo A. R., Nakamura H. GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution. Biophysics 8, 79-94, 2012.


Yamasaki H., Nakamura H., Electron density based interaction energy estimation of the special pair in the photosynthetic reaction center. Chem. Phys. Lertt. 536, 129-135, 2012.


Koizumi K., Shigeta Y., Okuyama O., Nakamura H., Takano Y., Coordination effects on the electronic structure of the CuA site of cytochrome c oxidase. Chem. Phys. Lett. 531, 197-201, 2012.


Kinjo A. R., Nakamura H., Composite Structural Motifs of Binding Sites for Delineating Biological Functions of Proteins. PLoS ONE 7, e31437, 2012.


Umezawa K., Ikebe J., Takano M., Nakamura H., Higo J., Conformational Ensembles of An Intrinsically Disordered Protein pKID with and without a KIX Domain in Explicit Solvent Investigated by All-Atom Multicanonical Molecular Dynamics. Biomolecules, 2, 104-121, 2012.


Yamanaka S., Kanda K., Saito T., Kitagawa K., Kawakami T., Ehara M., Okumura M., Nakamura H., Yamaguchi K. Does B3LYP correctly describe magnetism of manganese complexes with various oxidation numbers and various structural motifs? Chem. Phys. Lett. 519-520, 134-140, 2012.


Kinjo A. R., Suzuki H., Yamashita R., Ikegawa Y., Kudou T., Igarashi R., Kengaku Y., Cho H., Standley D. M., Nakagawa A., Nakamura H., Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. Nucleic Acids Research 40, D453-D460, 2012.


Berman H. M., Kleywegt G. J., Nakamura H., Markley J. L., The future of the protein data bank. Bioplymers, 99, 218-222, 2012.


Fukuda I., Nakamura H., Non-Ewald methods: Theory and Applications to Molecular Systems. Biophysical Reviews, 4, 161-170, 2012.


Kuroda D., Shirai H., Jacobson M. P., Nakamura H., Computer-aided antibody design. Protein Engineering, Design & Selection, 25, 507-522, 2012.


Berman H. M., Kleywegt G. J., Nakamura H., Markley J. L., The Protein Data Bank at 40: Reflecting on the Past to Prepare for the Future. Structure, 20, 391-396, 2012.


Higo J., Ikebe J., Kamiya N., Nakamura H., Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes. Biophysical Reviews, 4, 27-44, 2012.


Fleishman S. J., Whitehead T. A., Strauch E.-M., Corn J. E., Qin S., Zhou H.-X., Mitchell J. C., Demerdash O. N. A., Takeda-Shitaka M., Terashi G., Moal I. H., Li X., Bates P. A., Zacharias M., Park H., Ko J.-S., Lee H., Seok C., Bourquard T., Bernauer J., Poupon A., Azé J., Soner S., Ovalı S. K., Ozbek P., Tal N. B., Haliloglu T., Hwang H., Vreven T., Pierce B. G., Weng Z., Pérez-Cano L., Pons C., Fernández-Recio J., Jiang F., Yang F., Gong X., Cao L., Xu X., Liu B., Wang P., Li C., Wang C., Robert C. H., Guharoy M., Liu S., Huang Y., Li L., Guo D., Chen Y., Xiao Y., London N., Itzhaki Z., Schueler-Furman O., Inbar Y., Potapov V., Cohen M., Schreiber G., Tsuchiya Y., Kanamori E., Standley D. M., Nakamura H., Kinoshita K., Driggers C. M., Hall R. G., Morgan J. L., Hsu V. L., Zhan J., Yang Y., Zhou Y., Kastritis P. L., Bonvin A. M. J. J., Zhang W., Camacho C. J., Kilambi K. P., Sircar A., Gray J. J., Ohue M., Uchikoga N., Matsuzaki Y., Ishida T., Akiyama Y., Khashan R., Bush S., Fouches D., Tropsha A., Esquivel-Rodríguez J., Kihara D., Stranges P. B., Jacak R., Kuhlman B., Huang S.-Y., Zou X., Wodak S. J., Janin J., Baker D., Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J. Mol. Biol., 414, 289-302, 2011.


Wada M., Kanamori E., Nakamura H., Fukunishi Y., Selection of in-silico drug screening results for G-protein-coupled receptors by using universal active probe. J. Chem. Inf. Model., 51, 2398-2407, 2011.


Takano Y., Shigeta Y., Koizumi K., Nakamura H., Electronic Structures of the Cu2S2 Core of the CuA Site in Cytochrome c Oxidase and Nitronous Oxide Reductase. Int. J. Quantum Chem., 112, 208-218, 2011.


Fukunishi Y., Mizukoshi Y., Takeuchi K., Shimada I., Takahashi H., Nakamura H., Protein-ligand docking guided by ligand pharmacophore-mapping experiment by NMR. J. Mol. Graph. Model., 31, 20-27, 2011.


Dasgupta B., Nakamura H., Kinjo A. R., Distinct Roles of Overlapping and Non-overlapping Regions of Hub Protein Interfaces in Recognition of Multiple Partners. J. Mol. Biol. 411, 713-727, 2011.


Higo J., Nishimura Y., Nakamura H., A Free-Energy Landscape for Coupled Folding and Binding of an Intrinsically Disordered Protein in Explicit Solvent from Detailed All-Atom Computations. J. Ame. Chem. Soc., 133, 10448-10458, 2011.


Fukunishi Y., Nakamura H., Definition of drug-likeness for compound affinity. J. Chem. Inf. Model., 51, 1012-1016, 2011.


Fukuda I., Yonezawa Y., Nakamura H., Molecular dynamics scheme for precise estimation of electrostatic interaction via zero-dipole summation principle. J. Chem. Phys., 134, 164107, 2011.


Lis M., Kim T., Sarmiento J. J., Kuroda D., Dinh H. V., Kinjo A. R., Amada K., Devadas S., Nakamura H., Standley D. M., Bridging the gap between single-template and fragment based protein structure modeling using Spanner. Immunome Res., 7, 1-8, 2011.


Yonezawa Y., Fukuda I., Kamiya N., Shimoyama H., Nakamura H., Free Energy Landscapes of Alanine Dipeptide in Explicit Water Reproduced by the Force-Switching Wolf Method. J. Chem. Theory Comput., 7, 1484-1493, 2011.


Kanda K., Yamanaka S., Saito T., Umeda Y., Kawakami K., Shen J.-R., Kamiya N., Okumura M., Nakamura H., Yamaguchi K., Labile electronic and spin states of the CaMn4O5 cluster in the PSII system refined to the 1.9 A X-ray resolution. UB3LYP computational results. Chem. Phys. Lett., 506, 98-103, 2011.


Ikebe J.,Umezawa K., Kamiya K., Sugihara T., Yonezawa Y., Takano Y., Nakamura H., Higo J., Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water. J. Comput. Chem. 32, 1286-1297, 2011.


Yonezawa Y., Standley D. M., Nakamura H., Degree of Pyramidality Governs the Height and Peak position of the Free-Energy-Barrier for the cis-trans Isomerization of N-Methylacetamide. Chem. Phys. Lett. 503, 139-144, 2011.


Takano Y., Yonezawa Y., Fujita Y., Kurisu G., Nakamura H., Intrinsic Electronic Structures of the Novel [4Fe–4S] Cluster Found in Dark-operative Protochlorophyllide Oxidoreductase (DPOR). Chem. Phys, Lett. 503, 296-300, 2011.


Shimoyama H., Nakamura H., Yonezawa Y. Simple and effective application of the Wang-Landau method for multicanonical molecular dynamics simulation. J. Chem. Phys. 134, 024109, 2011.


Yonezawa Y., Shimoyama H., Nakamura H., Multicanonical Molecular Dynamics Simulations Combined with MetaDynamics for the Free Energy Landscape of a Biomolecular System with High Energy Barriers. Chem. Phys. Lett. 501, 598-602, 2011.


Patil A., Nakai K., Nakamura H., HitPredict: a database of quality assessed protein-protein interactions in 9 species. Nucleic Acids Research 39, D744-D749, 2011.


Kanamori E., Igarashi S., Osawa M., Fukunishi Y., Shimada I., Nakamura H., Structure determination of a protein assembly by amino acid selective cross-saturation. PROTEINS 79, 179-190, 2011.


Ikebe J., Standley D. M., Nakamura H., Higo J., Ab initio simulation of a 57-residue protein in explicit solvent reproduces the native conformation in the lowest free-energy cluster. Protein Science, 20, 187-196, 2011.


Fukunishi Y., Nakamura H., Prediction of ligand-binding sites of proteins by the probe-docking binding-site finding (ProbeSite) method. Protein Science, 20, 95-106, 2011.


Shiga D., Nakane D., Inomata T., Funahashi Y., Masuda H., Kikuchi A., Oda M., Noda M., Uchiyama S., Fukui K., Kanaori K., Tajima K., Takano Y., Nakamura H., Tanaka T. Creation of a Type 1 Blue Copper Site within a de Novo Coiled-coil Protein Scaffold. J. Am. Chem. Soc. 132, 18191-18198, 2010.


H. Shimoyama, Y. Yonezawa, H. Nakamura  (2010) Enhanced free-energy calculation using multi-scale simulation. J. Chem. Phys. 133, 135101.


A. R. Kinjo, R. Yamashita, H. Nakamura (2010) PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan, Database 2010, ID baq021,


A. Patil, K. Kinoshita, H. Nakamura (2010) Domain distribution and intrinsic disorder in hubs in the human protein-protein interaction network. Protein Science 19 (8), 1461-1468.


Y. Murakami, Ruth Spriggs, H. Nakamura, S. Jones (2010) PiRaNhA: a server for the computational prediction of RNA-binding residues in protein. Nucl. Acids Res. 38 (Web server issue) W412-416.


Y. Fukunishi, K. Ono, M. Orita, H. Nakamura (2010) Selection of in-silico drug screening result by using universal active probes (UAPs). J. Chem. Inf. Model. 50 (7) 1233-1240


A. R. Kinjo, H. Nakamura (2010) Geometric similarities of protein-protein interfaces at atomic resolution are only observed within homologous families: An exhaustive structural classification study, J. Mol. Biol. 399 (3) 526-540.


K. Umezawa, R. Morikawa, H. Nakamura, J. Higo (2010) Solvent flow patterns fluctuating largely around a protein and correlation with solvent density fluctuations: a molecular dynamics study. J. Chem. Phys. 132(15) 155103.


T. Mashimo, Y. Fukunishi, M. Orita, N. Katayama, S. Fujita, H. Nakamura (2010) Quantitative analysis of aggregation-solubility relationship by in-silico solubility prediction. International Journal of High Throughput Screening 2010:1, 99-107.


A. Patil, K. Kinoshita, H. Nakamura (2010) Structural properties of hubs in protein-protein interaction networks. Int. J. Mol. Sci. 11(4), 1930-1943.


D. M. Standley, R. Yamashita, A. R. Kinjo, H. Toh, H. Nakamura: SeSAW (2010) balancing sequence and structural information in protein function mapping. Bioinformatics 26 (9) 1258-1259.


Y. Takano, H. Nakamura (2010) Electronic structures of heme a of cytochrome c oxidase in the redoc states –Charge density migration to the propionate groups of heme a-. J. Comput. Chem.  31 (5) 954-962.


S. Yamanaka, S. Nishihara, K. Nakata, Y. Yonezawa, M. Okumura, T. Takada, H. Nakamura, K. Yamaguchi (2009) Resonating coupled-cluster CI approach to Ion-radical systems:Comparison with the unrestricted coupled-cluster approach. Int J Quantum Chem. 109, 3811-3818.


D. Shiga, D. Nakano, T. Inomata, H. Masuda, M. Oda, Y. Takano, H. Nakamura, T. Mizuno, T. Tanaka (2009) Design of the distorted coordination structure of Cu2+ in a de novo designed protein. Biopolymers 91, 907-916.


Y. Takano, H. Nakamura (2009) Density functional study of roles of porphyrin ring in electronic structures of heme. Int. J. Quantum Chem. 109, 3583-3591.


Y. Takano, K. Koizumi, H. Nakamura (2009) Theoretical studies of the magnetic couplings and the chemical indices of the biomimetic models of oxyhemocyanin and oxytyrosinase. Inorganica Chim Acta  362  (12) 4578-4584.


Y. Fukunishi, D. Mitomo, H. Nakamura  (2009) ProteinLigand Binding Free Energy Calculation by the Smooth Reaction Path Generation (SRPG) Method. J. Chem. Inf. Model. 49 (8) 1944–1951.


T. Sugihara, J. Higo, H. Nakamura (2009) Parallelization of Markov Chain Generation and its Application to the Multicacnonical Method. J. Phys. Soc. Jpn. 78 (7) 074003.R. Apostolov, Y. Yonezawa,


D. M. Standley, G. Kikugawa, Y. Takano, H. Nakamura (2009) Membrane attachment facilitates ligand access to active site in Monoamine oxidase A. Biochemistry 48 (25)  5864-5873.


R. V. Spriggs, Y. Murakami, H. Nakamura, S. Jones (2009) Protein function annotation from sequence, PiRaNhA: prediction of specific RNA-binding residues. Bioinformatics 25 (12) 1492-1497.


J. Higo, N. Kamiya, T. Sugihara, Y. Yonezawa, H. Nakamura (2009) Verifying trivial parallelization of multicanonical molecular dynamics for conformational sampling of a polypeptide in explicit water. Chem. Phys. Lett. 473 (4-6) 326–329. Y.


Fukunishi, T. Mashimo, M. Orita, K. Ohno, H. Nakamura (2009) In-silico fragment screening by replica generation (FSRG) method for fragment-based drug design. J. Chem. Inf. Model. 49 (4), 925-933.


K. Koizumi, K. Yamaguchi, H. Nakamura, Y. Takano (2009) Hybrid-DFT study on electronic structures of the active site of sweet poteto purple acid phosphatase –The origin of stronger antiferromagnetic coupling than other purple acid phosphatase- J. Phys. Chem. A 113 (17) 5099-5104.


K. Matsushita, O. Takeuchi, D. M. Standley, Y. Kumagai, T. Kawagoe, T. Miyake, T. Sato, H. Kato, T. Tsujimura, H. Nakamura, S. Akira (2009) The CCCH-type zinc finger protein, Zc3h12a, is a ribonuclease essential for controlling immune responses by regulating mRNA decay. Nature,  458, 1185-1190.


Y. Yonezawa, K. Nakata, K. Sakakura, T. Takada, H. Nakamura (2009) Intra- and Intermolecular Interaction Inducing Pyramidalization on both sides of a Proline Di-peptide during Isomerization: an ab Initio QM/MM Molecular Dynamics Simulation Study in explicit water. J. Ame. Chem. Soc. 131 (12) 4535-4540.


K. Umezawa, J. Ikebe, M. Nomizu, H. Nakamura, J. Higo (2009) Conformational requirement on peptides to exert laminin’s activities and search for protein segments with the laminin’s activities. Biopolymers: Peptide Science 92 (2), 124-131.


S. Queyroy, I. Fukuda, H. Nakamura (2009) Numerical examination of the extended phase-space volume-preserving integrator by the Nose-Hoover molecular dynamics equations. J. Comput. Chem. 30 (12) 1799-1815.


S. Nishihara, S. Yamanaka, K. Nakata, y. Kitagawa, Y. Yonezawa, M. Okumura, H. Nakamura, T. Takada, K. Yamaguchi (2009) A resonating broken-symmetry CI study of cationic states of phenalenyl dimeric compounds. Polyhedron 28 (9-10), 1628-1633.


S. Nishihara, S. Yamanaka, K. Kusakabe, K. Nakata, Y. Yonezawa, H. Nakamura, T. Takada, K. Yamaguchi (2009) A resonating broken symmetry CI approach for double-exchange magnetic systems. J. Phys. Cond. Matter  21, 064227.


A. R. Kinjo, H. Nakamura (2009) Comprehensive structural classification of ligand binding motifs in proteins. Structure 17 (2), 234-246.


D. Kuroda, H. Shirai, M. Kobori, H. Nakamura (2009) Systematic classification of CDR-L3 in antibodies: Implications of the light chain sub-types and the VL-VH interface. PROTEINS  75 (1), 139-146.


Y. Fukunishi, H. Nakamura (2009) A new method for in-silico drug screening and similarity search using molecular-dynamics maximum-volume overlap (MD-MVO) method. J. Mol. Graph. Modelling 27,  628-636.


G. Kikugawa, R. Apostolov, N. Kamiya, M. Taiji, R. Himeno, H. Nakamura, Y. Yonezawa (2009) Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems. J. Comput. Chem. 30, 110-118.


S. Date, K. Nozaki, H. Nakamura, S. Sakoda, S. Shimojo (2008) A grid-aware access control mechanism in a clinical database for Parkinson’s disease research and diagnosis. IPSJ Trans. Bioinfo. 1 (Nov.), 42-52.


I. Fukuda, Y. Yonezawa, H. Nakamura (2008) Consistent molecular dynamics scheme applying the Wolf summation for calculating electrostatic interaction of particles. J. Phys. Soc. Jpn. 77 (11), 114301.


S. Nishihara, S. Yamanaka, T. Ukai, K. Nakata, K. Kusakabe, Y. Yonezawa, H. Nakamura, T. Takada, K. Yamaguchi (2008) Resonating broken symmetry CI approach for ion-radical systems: Comparison with UHF, hybrid-DFT, and CASSCF-DFT. Int. J. Quant. Chem. 109 (15), 2966-2977.


H. Yamasaki, Y. Takano, H. Nakamura (2008)  Theoretical investigation of the electronic asymmetry of the special pair cation radical in the photosynthetic type-II reaction center. J. Phys. Chem. B  112 (44), 13923-13933.


D. Kuroda, H. Shirai, M. Kobori, H. Nakamura (2008) Structural classification of CDR-H3 revisited: a lesson in antibody modeling. PROTEINS 73 (3), 15 Nov., 608-620.


D. M. Standley, H. Toh, H. Nakamura (2008) Functional annotation by sequence-weighted strutture alignments: Statistical analysis and case studies from the Protein 3000 structural genomics project in Japan. PROTEINS  72 (4), 1333-1351.


D. M. Standley, A. R. Kinjo, K. Kinoshita, H. Nakamura (2008) Protein structure databases with new Web services for structural biology and biomedical research. Briefings in Bioinformatics  9 (4), 276-285.


A. R. Kinjo, H. Nakamura (2008) Nature of protein family signatures: Insights from singular value analysis of position-specific scoring matrices. PLoS ONE  3 (4), e1963.


J. L. Markley, E. L. Ulrich, H. M. Berman, K. Henrick, H. Nakamura, H. Akutsu (2008) BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions. J. Biomol NMR  40 (1), 153-155.


Y. Fukunishi, H. Nakamura (2008) Improvement of protein-compound docking scores by using amino-acid sequence similarities of proteins. J. Chem. Inf. Model. 48 (1), 148-156.


Y. Fukunishi, H. Nakamura (2008) Prediction of protein-ligand complex structure by docking software guided by other complex structures. J. Mol. Graph. Model.  26 (6), 1030-1033.


K. Henrick, Z. Feng, W. F. Bluhm, D. Dimitropoulos, J. F. Doreleijers, S. Dutta, J. L. Flippen-Anderson, J. Ionides, C. Kamada, E. Krissinel, C. L. Lawson, J. L. Markley, H. Nakamura, R. Newman, Y. Shimizu, J. Swaminathan, S. Velankar, J. Ory, E. L. Ulrich, W. Vranken, J. Westbrook, R. Yamashita, H. Yang, J. Young, M. Yousufuddin, H. M. Berman (2008) Remeidation of the protein data bank archive. Nucl. Acids Res. 36, D426-D433.


N. Kamiya, Y. Yonezawa, H. Nakamura, J. Higo (2008) Protein-inhibitor flexible docking by a multicanonical sampling: Native complex structure with the lowest free energy and a free-energy barrier distrinsuishing the native complex from the others. PROTEINS 70 (1), 41-53.


A. R. Kinjo, H. Nakamura (2007) Similarity search for local protein structures at atomic resolution by exploiting a database management system. Biophysics 3, 75-84.


E. Kanamori, Y. Murakami, Y. Tsuchiya, D. M. Standley, H. Nakamura, K. Kinoshita (2007) Docking of protein molecular surfaces with evolutionary trace analysis. PROTEINS  69 (4), 832-838.


H. Yamasaki, H. Nakamura, Y. Takano (2007) Theoretical analysis of the electronic asymmetry of the special pair in the photosynthetic reaction center: Effect of the protein environment and structural asymmetry. Chem. Phys. Lett.  447 (4-6), 324-329.


J. Ikebe, N. Kamiya, H. Shindo, H. Nakamura, J. Higo (2007) Conformational sapling of a 40-residue protein consisting of a and b secondary-structure elements in explicit solvent. Chem. Phys. Lett. 443 (4-6), 364-368.


A. Patil, H. Nakamura (2007) The role of charged surface residues in the binding ability of small hubs in protein-protein interaction networks. BIOPHYSICS  3,  27-35.


K. Kinoshita, Y. Murakami, H. Nakamura: eF-seek (2007) Prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape. Nucl. Acids Res. 35, W398-W402.


S. Date, T. Tashiro, K. Nozaki, H. Nakamura, S. Sakoda, S. Shimojo (2007) A Grid-ready Clinical Database for Parkinson's Disease Researchand Diagnosis. The 20th IEEE International Symposium on Computer-Based Medical Systems, in press. (


D. M. Standley, H. Toh, H. Nakamura (2007) ASH structure alignment package: Sensitivity and selectivity in domain classification. BMC Bioinformatics 8, 4-April-2007, 116


Y. Fukunishi, S. Kubota, H. Nakamura (2007) Finding ligands for G-protein coupled receptors based on the protein-compound affinity matrix. J. Mol. Graph. Modelling 25 (5), 633-643.


H. Berman, K. Henrick, H. Nakamura, J. L. Markley (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucl. Acids Res. 35 (Database Isssue), D301-D303.


K. Sukegawa-Hayasaka, Z. Kato, H. Nakamura, S. Tomatsu, T. Fukao, K. Kawata, T.Orii, N. Knodo (2006) Effect of Hunter Disease mutations on molecular phenotypes of iduronate-2-sulfonate: Enzymatic activity, protein processing and structural analysis. J. Inherit Metab. Dis. 29, 755-761.


Y. Fukunishi, S. Hojo, H. Nakamura (2006) An efficient in silico screening method based on the protein-compound affinity matrix and its application to the design of a focused library for cytochrome P450 (CYP). Journal of Chemical Information and Modeling  46 (6), 2610-2622.


Y. Fukunishi, S. Kubota, C. Kanai, H. Nakamura (2006) A virtual active compound produced from the negative image of a ligand-binding pocket, and its application to in-silico drug screening. J. Computer-Aided Mol. Design 20 (4), 237-248.


Y. Takano, H. Nakamura: Quantum mechanical study of the proton transfer via a peptide bond in the novel proton translocation pathway of cytochrome c oxidase. Chem. Phys. Lett. (2006) 430 (1-3), 149-155.


Y. Fukunishi, S. Kubota, H. Nakamura: Noise reduction method for molecular interaction energy: Application to in silico drug screening and in silico target proteins creening.  Journal of Chemical Information and Modeling (2006) 46 (5), 2071-2084.


Y. Yonezawa, K, Nakata, T. Takada, H. Nakamura: Molecular Dynamics Simulation Study on Water Associated with π-electrons of Benzene by using QM/MM Potential. Chem. Phys. Lett. (2006) 428 (1-3),73-77.


Y. Tsuchiya, K. Kinoshita, H. Nakamura (2006) Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity. Protein Engineering, Design and Screening  19 (9), 421-429.


Y. Tsuchiya, K. Kinoshita, N. Ito, H. Nakamura (2006) PreBI : Prediction of biological interfaces of proteins in crystals. Nucl. Acids Res. 34 (Web Server issue), W20 - W24.


P. Gou, G. T. Hanke, Y. Kimata-Ariga, D. M. Standley, A. Kubo, I. Taniguchi, H. Nakamura, T. Hase (2006) Higher order structure contributes to specific differences in redox potential and electron transfer efficiency of root and leaf Ferredoxins. Biochemistry 45 (48), 14389-14396.


D. M. Standley, Y. Yonezawa, Y. Goto, H. Nakamura (2006) Flexible docking of an amyloid-forming peptide from beta-2-microglobulin. FEBS Letters 580 (26), 6199-6205.


Y. Katoh, H. Takemori, X.-Z. Lin, M. Tamura, M. Muraoka, T. Satoh, Y. Tsuchiya, L. Min, J. Doi, A. Miyauchi, L. A. Witters, H. Nakamura, M. Okamoto (2006) Silencing the constitutive active transcription factor CREB by the LKB1-SIK signaling cascade. FEBS Journal 273 (12), 2730-2748.


Y. Fukunishi, Y. Mikami, S. Kubota, H. Nakamura (2006) Multiple target screening method for robust and accurate in silico ligand screening. J. Mol. Graph. Modelling 25 (1), 61-70.


H. Takahashi, M. Miyazawa, Y. Ina, Y. Fukunishi, Y. MIzukoshi, H. Nakamura, I. Shimada (2006) Utilization of methyl proton resonances in cross-saturation measurement for determining the interfaces of large protein-protein complexes. J. Biomolecular NMR 34 (3), 167-177.


A. Patil, H. Nakamura (2006) Disordered domains and high surface charge confer hubs with the ability to interact with multiple proteins in interaction networks. FEBS Letters 580 (8) 03-April-2006, 2041-2045.


I. Fukuda, H. Nakamura (2006) Construction of an extended invariant for an arbitrary ordinary differential equation with its development in a numerical integration algorithm. Phys. Rev. E. 73 (2), 026703.


Y. S. Watanabe, Y. Fukunishi, H. Nakamura (2006) Generation of a flexible loop structural ensemble and its application to induced-fit structural changes following ligand binding. BIOPHYSICS 2 (1), 1-12.


Y. Fukunishi, Y. Mikami, K. Takedomi, M. Yamanouchi, H. Shima, H. Nakamura (2006) Classification of chemical compounds by protein-compound docking for use in designing a focused library. J. Med. Chem. 49 (2), 523-533.


D. M. Standley, H. Toh, H. Nakamura(2005) GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures. BMC Bioinformatics 6,  08-Sep-2005, 221.


Y. Fukunishi, Y. Mikami, H. Nakamura (2005) Similarities among receptor pockets and among compounds: Analysis and application to in silico ligand screening. J. Mol. Graph. Modelling 24 (1), 34-45.


A. Patil, H. Nakamura (2005) Filtering high-throughput protein-protein interaction data using a combination of genomic features. BMC Bioinformatics 6, 100.


I. Fukuda, H. Nakamura (2005) Molecular dynamics sampling scheme realizing multiple distributions. Phys. Rev. E 71, 046708.


Y. Tsuchiya, K. Kinoshita, H. Nakamura (2005) PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces. Bioinformatics 21, 1721-1723.


J. Westbrook, N. Ito, H. Nakamura, K. Henrick, H. M. Berman (2005) PDBML: The representation of archival macromolecular structure data in XML. Biooinformatics 21, 988-992.


I, Fukuda, M. Horie, H. Nakamura (2005) Deterministic design for Tsallis distribution sampling. Chem. Phys. Lett. 405, 364-370.


A. Patil, H. Nakamura (2005) HINT: a database of annotated protein-protein interactions and their homologs. BIOPHYSICS 1, 21-24.


K. Kinoshita, H. Nakamura (2005) Identification of the ligand binding sites on the molecular surface of proteins. Protein Science 14, 711-718.


J. G. Kim, Y. Fukunishi, A. Kidera, H. Nakamura (2004) Multicanonical molecular dynamics algorithm employing an adaptive force-biased iteration scheme. Phys. Rev. E 70, 57103.


Y. S. Watanabe, J. G. Kim, Y. Fukunishi, H. Nakamura (2004) Free energy landscapes of small peptides in an implicit solvent model determined by force-biased multicanonical molecular dynamics simulation. Chem. Phys. Lett. 400, 258-263.


R. Tatsumi, Y. Fukunishi, H. Nakamura (2004) A hybrid method of molecular dynamics and harmonic dynamics for dockinig of flexible ligand to flexible receptor. J. Comput. Chem. 25, 1995-2005.


J. G. Kim, Y. Fukunishi, A. Kidera, H. Nakamura (2004) Generalized simulated tempering realized on expanded ensembles of non-Boltzman weights. J. Chem. Phys. 121, 5590-5601.


J. G. Kim, Y. Fukunishi, H. Nakamura (2004) Dynamical origin of enhanced conformational searches of Tsallis statistical sampling. J. Chem. Phys. 121, 1626-1635.


J. G. Kim, Y. Fukunishi, H. Nakamura (2004) Average energy guided simulated tempering implemented into molecular dynamics algorithm for protein folding simulation. Chem. Phys. Lett. 392, 34-39.


I. Fukuda, H. Nakamura (2004) Efficiency in Generation of the Boltzmann-Gibbs Distribution by the Tsallis Dynamics Re-weighting Method. J. Phys. Chem. B 108, 4162-4170.


D. M. Standley, H. Toh, H. Nakamura (2004) Detecting local structural similarity in proteins by maximizing number of equivalent residues. PROTEINS 57, .381-391.


T. Matsuda, T. Ikegami, N. Nakajima, T. Yamazaki, and H. Nakamura (2004) Model building of a protein-protein complexed structure using saturation transfer and residual dipolar coupling without paired intermolecular NOE. J. Biomol. NMR 29, 325-338.


Y. S. Watanabe, Y. Fukunishi, H. Nakamura (2004) Modelling of third cytoplasmic loop of bovine rhodopsin by multicanonical molecular dynamics. J. Mol. Graph. Model. 23, 59-68.


Y. Tsuchiya, K. Kinoshita, H. Nakamura (2004) Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces. PROTEINS 55, 885-894.


K. Kinoshita, H. Nakamura: eF-site and PDBjViewer (2004) dtabase and  viewer for protein functional sites. Bioinformatics 20, 1329-1330.


T. Matsuda, N. Nakajima, T. Yamazaki, and H. Nakamura (2004) CAD-ICAD complex structure derived from saturation transfer experiment and simulated annealing without using pairwise NOE information. J. Mol. Recognit. 17, 41-50.


H. Nakamura, S. Date, H. Matsuda, and S. Shimojo (2004) A challenge towards next-generation research infrastructure for advanced life science. New Generat. Comput. 22, 157-166.


H. Berman, K. Henrick, H. Nakamura (2003) Announcing the worldwide Protein Data Bank. Nature Struct. Biol. 10, 980.


I. Fukuda, H. Nakamura (2003) Deterministic generation of the Boltzmann-Gibbs distribution and the free energy calculation form the Tsallis distribution. Chem. Phys. Lett. 382, 367-373.


Y. Fukunishi, Y. Mikami, H. Nakamura (2003) The filling potential method: a method for estimating the free energy surface for protein-ligand docking. J. Phys. Chem. B 107, 13201-13210.


K. Takeuchi, M. Yokogawa, T. Matsuda, M. Sugai, S. Kawano, T. Khono, H. Nakamura, H. Takahashi, I. Shimada (2003) Structural basis of the KcsA K+ channel and agitoxin2 pore-blocking toxin interaction by using the transferred cross-saturation method. Structure 11, 1381-1392.


J. Hirayama, H. Nakamura, T. Ishikawa, Y. Kobayashi, and T. Todo (2003) Functional and structural analyses of cryptochrome: Vertebrate CRY regions responsible for the interaction with the CLOCK:BMAL1 heterodimer and its nuclear localization. J. Biol. Chem. 278, 35620-35628.


J. G. Kim, Y. Fukunishi, A. Kidera, H. Nakamura (2003) Determination of multicanonical weight based on stochastic model of sampling dynamics. Phys. Rev. E 68, 21110.


A. M. Montano, I. Kaitila, K. Sukegawa, S. Tomatsu, Z. Kato, H. Nakamura, S. Fukuda, T. Orii, N. Kondo (2003) Mucopolysaccharidosis IVA: characterization of a common mutation found in Finnish patients with attenuated phenotype. Human Genet. 113, 162-169.


N. Handa,T. Terada, Y. Kamewari, H. Hamana, J.R.H. Tame, S.-Y. Park, K. Kinoshita, M. Ota,H. Nakamura, S. Kuramitsu, M. Shirouzu, S. Yokoyama (2003) Crystal structure ofthe conserved protein TT1542 from Thermus thermophilus HB8. Protein Science 12:1621-1632.


K. Kinoshita,H. Nakamura (2003) Identification of protein biochemical functions bysimilarity search using the molecular surface database, eF-site. ProteinScience, 12: 1589-1595.


K. Kinoshita, H. Nakamura (2003) Protein informaticstowards function identification. Curr. Opin. Struct. Biol., 13: 396-400.


J. G. Kim, Y. Fukunishi, H. Nakamura (2003) Dynamicalorigin of uniform sampling in multicanonical ensemble, Phys. Rev. E, 67: 11105.


K. Ikeda,O. V. Galzitskaya, H. Nakamura, J. Higo (2003) Beta-hairpins, alpha-helices,and the intermediates among the secondary structures in the energy landscape ofa peptide from a distal beta-hairpin of SH3 domain. J. Comput. Chem., 24:310-318.


N.Ito, H. Sakamoto, K. Kobayashi, H. Nakamura (2002) New Features of PDBj-ML, anXML Format for Protein Data Bank. Genome Informtaics, 13: 488-489.


Y. Tsuchiya, K. Kinoshita, H. Nakamura (2002) Analysis ofComplementarity of Protein-DNA Interactions Using the Electrostatic Potentialand the Molecular Surface Geometry. Genome Informtaics, 13: 310-311.


N. Kamiya,J. Higo, H. Nakamura (2002) Conformational transition states of beta-hairpinpeptide between the ordered and disordered conformations in explicit water.Protein Science, 11: 2297-2307.


K. Matsushita, K. Kinoshita, T. Matsuoka, A. Fujita,T. Fujikado, Y. Tano, H. Nakamura, Y. Kurachi (2002) Intermolecular interaction of SUR2 subtypesfor intracellular ADP-induced differential control of K-ATP channels. CirculationResearch, 90: 554-561.


I. Fukuda and H.Nakamura (2002) Tsallis dynamics using Nose-Hoover approach. Phys. Rev. E, 65:26105.


K. Kinoshita, J.Furukawa and H. Nakamura (2002) Identification of protein functions from amolecular surface database, eF-site. J. Struct. Funct. Genomics. J. Struct.Funct. Genomics, 2: 9-22.


S. Ono, M. Kuroda, J.Higo, N. Nakajima and H. Nakamura (2002) Calibration of force-field dependencyin free energy landscapes of peptide conformations by quantum chemicalcalculations. J. Comput. Chem., 23: 470-476.


J.Higo, Y. Sugimoto, K. Wakabayashi, H. Nakamura (2001) Collective  motions of myosin head derived frombackbone molecular dynamics and combination with X-ray solution scatteringdata. J. Comput. Chem., 22: 1983-1994.


N. Ito, H. Sakamoto,K. Kobayashi, H. Nakamura(2001) Development of PDBj-ML. Genome Informatics, 12:508-509.


K. Kinoshita, Y.Tsuchiya, H. Nakamura (2001) Analysis of complementarity of protein-protein andprotein-DNA interactions using the molecular surface database, eF-site. GenomeInformatics, 12: 345-347.


K. Furukawa, H.Shirai, T. Azuma and H. Nakamura (2001) A role of the third complementaritydetermining region in the affinity maturation of an antibody. J. Biol. Chem.,276: 27622-27628.


J. Higo, M. Sarai, H.Shirai, H. Nakamura and T. Kugimiya (2001) Large vortex-like structure ofdipole field in computer models of liquid water and dipole-bridge betweenbiomolecules. Proc. Natl. Acad. Sci. USA, 98: 5961-5964.


J. Higo, N. Ito, M.Kuroda, S. Ono, N. Nakajima and H. Nakamura (2001) Energy landscape of apeptide consisting of alpha-helix, 3(10)-helix, beta-turn, beta-hairpin, andother disordered conformations. Protein Science, 10: 1160-1171.


J. Higo, O.V. Galzitskaya,S. Ono and H. Nakamura (2001) Energy landscape of a beta-hairpin peptide inexplicit water studied by multicanonical molecular dynamics. Chem. Phys. Lett.377: 169-175.


Y. Yamagata, K.Ogasawara, Y. Hioki, S.J. Lee, A. Nakagawa, H. Nakamura, M. Ishida, S.Kuramitsu and K. Yutani (2001) Entropic stabilization of the tryptopan syntasealpha-subunit from a hyperthermopile, Pyrococcus furiosus. J. Biol. Chem. 276:11062-11071.


K. Hitomi, H.Nakamura, S.-T. Kim, T. Mizukoshi, T. Ishikawa, S. Iwai and T. Todo ( 2001)Role of two histidines in the (6-4) photolyase reaction. J. Biol. Chem. 276:10103-10109.


A.R. Kinjo, A. Kidera,H. Nakamura and K. Nishikawa (2001) Physicochemical evaluation of protein foldspredicted by threading. Eur. Biophys. J. 30: 1-10.


S. Yamamoto-Katayama,A. Sato, M. Ariyoshi, M. Suyama, K. Ishikhara, T. Hirano, H. Nakamura, K.Morikawa and H. Jingami (2001) Site-directed removal of N-glycosylation sitesin BST-1/CD157: Effects on molecular and functional heterogeneity. Biochem. J.,357: 385-392.


T. Fukao, G.A.Mitchell, X.-Q. Song, H. Nakamura, J.E. Wraith, G. Besley, R.J.A. Wanders, K.E.Niezen-Koning, G.T. Berry, M. Palmieri, S. Kassovska-Bratinova, K.E. Orii andN. Kondo (2000) Succinyl-CoA:3-ketoacid CoA transferase (SCOT): Cloning of thehuman SCOT gene, tertiary structural modelling of the human SCOT monomer andcharacterization of three pathogenic mutations. Genomics 68: 144-151.


K. Sukegawa, H.Nakamura, Z. Kato, S. Tomatsu, A.M. Montano, T. Fukao, G. Toietta, P. Tortora,T. Orii and N. Kondo (2000) Biochemical and structural analysis of missensemutations in N-acetylgalactosamine-6-sulfate sulfatase causingmucopolysaccharidosis IVA phenotypes. Human Mol. Genet. 9: 1283-1290.


M. Oda and H. Nakamura(2000) Thermodynamic and kinetic analyses for understanding sequence-sepcificDNA recognition (Review). Genes to Cells 5: 319-326.


S. Ono, N. Nakajima,J. Higo and H. Nakamura (2000) Peptide free energy profile is stronglydependent on the force field: Comparison of C96 and AMBER95. J. Comput. Chem.9: 748-762.


 O.V. Galzitskaya, J. Higo, M. Kuroda and H. Nakamura (2000)beta-hairpin folds by molecular dynamics simulations. Chem. Phys. Lett. 326:421-429.


 N. Nakajima, J. Higo, A. Kidera and H. Nakamura (2000) Free energylandscapes of peptides by enhanced conformational sampling. J. Mol. Biol. 296:197-216.


 O. V. Galzitskaya, A. K. Surin, and H. Nakamura: Optimum region ofaverage side-chain entropy for fast protein folding. Protein Science (2000) 9,580-586.


N. Nakajima, J. Higo,A. Kidera, and H. Nakamura: Free energy landscapes of peptides by enhancedconformational sampling. J. Mol. Biol. (2000) 296, 197-216.


H. Nakamura, S. Ono,and J. Higo: A general ab initio approach for free energy landscapes ofbiological molecules around the transition states: Fusion of the classicalmolecular mechanics simulation and the quantum chemical calculation. Proc.Japan Acad. (1999) 75, Ser.B, 291-294.


O. Ohkawa, D.Namihira, T. Maeda, N. Komoda, A. Kidera, and H. Nakamura: Classification andfeature extraction of protein structures based on structure transformation. Int.J. Artif. Intell. Tools (1999) 8, No. 2.  


S. Ono, N. Nakajima,J. Higo and H.Nakamura (1999) The multicanonical weighted histogram analysismethod for the free energy landscape along structural transition paths. Chem.Phys. Lett., 312, 247-254.


K. Furukawa, A.Akasako-Furukawa, H. Shirai, H. Nakamura, and T. Azuma (1999) Junctional aminoacids determine the maturation pathway of an antibody. Immunity, 11, 329-338.


S.T. Kim, H. Shirai,N. Nakajima, J. Higo, and H. Nakamura (1999) Enhanced conformational diversitysearch of CDR-H3 in antibodies: Roles of the first CDR-H3 residue. Proteins:Struct. Funct. and Genet., 37, 683-696.


M. Oda, K. Furukawa,A. Sarai, and H. Nakamura (1999) Construction of an artificial tandem proteinof the c-Myb DNA-binding domain and analysis of its DNA binding specificity.BBRC 262, 94-97.


H. Shirai, A. Kidera,and H. Nakamura (1999) H3-rules: Identification of CDR-H3 structures inantibodies. FEBS Lett. 455, 188-197.


M. Oda, K. Furukawa,A. Sarai and H. Nakamura (1999) Kinetic analysis of DNA binding by the c-MybDNA-binding domain using surface plasmon resonance. FEBS Lett., FEBS Lett. 454,288-292.


V.P. Repunte, H.Nakamura, A.Fujita, Y.Horio, I. Findlay, L. Pott and Y. Kurachi (1999)Extracellular links in Kir subunits conrol the unitary conductance ofSUR/Kir6.0 ion channels. EMBO J., 18, 3317-3324.


J. Higo, H. Kono, N.Nakajima, H. Shirai, H. Nakamura and A. Sarai (1999) Molecular dynamics studyon mobility and dipole ordering of solvent around proteins: effects ofperiodic-box size and protein charge. Chem. Phys. Lett. 306, 395-401.


Y. Koga, M. Morikawa, M.Haruki, H. Nakamura, T. Imanaka, and S. Kanaya (1998) Thermostable glycerolkinase from a hyperthermophilic archaeon: gen cloning and characterization ofthe recombinant enzyme. Protein Engineering 11, 1219-1227.


K. Suzuki, H. Hiroaki,D. Kohda, H. Nakamura and T. Tanaka (1998) Metal ion induced self-assembly of adesigned peptide into a triple-stranded a-helical bundle: A novel metal bindingsite in the hydrophobic core. J. Am. Chem. Soc. 120, 13008-13015.


T. Ohmura, H.Nakamura, K. Niki, M.A. Cusanovich, and H. Akutsu (1998) Ionicstrength-dependent physicochemical fac tors in cytochrome c3 regulating theelectron transfer rate. Biophys. J., 75, 1483-1490.


T. Mogi, M. Tsubaki,H. Hori, H. Miyoshi, H. Nakamura, and Y. Anraku (1998) Two terminal quinoloxidase families in Escherichia coli:: Variations on molecular machinery fordioxygen reduction. J. Biochem. Mol. Biol. & Biophys., 2, 79-110.


R.N.Z.A. Rahman, S.Fujuwara, H. Nakamura, M. Takagi and T. Imanaka (1998) Ion pairs involved inmaintaining a thermostable structure of glutamate dehydrogenase from ahyperthermophilic archaeon. Biochem. Biophys. Res. Comm. 248, 920-926.


T. Fukao, H. Nakamura,X-Q. Song, K. Nakamura, K. Orii, Y. Kohno, M. Kano, S. Yamaguchi, T. Hashimoto,T. Orii and N. Kondo (1998) Characterization of N93S, I312T, and A333P missensemutations in two Japanese families with mitochondorial acetoacetyl-CoA Thiolasedeficiency. Human Mutation 12, 245-254.


T. Yamazaki, T. Otomo,N. Oda, Y. Kyogoku, K. Uegaki, N. Ito, Y. Ishino and H. Nakamura (1998)Segmental isotope-labeling using peptide splicing for protein NMR. J. Am. Chem.Soc. 120, 5591-5592.


M. Hirose, T. Hayano,H. Shirai, H. Nakamura and M. Kikuchi (1998) Isolation of anti-glutathioneantibodies from a phage display library. Protein Engineering, 11, 243-248.


M. Kono, G. Miyazaki,H. Nakamura, Y. Wada and K. Imai (1998) Site-directed mutagenesis inhemoglobin: attempts to control the oxygen affinity with cooperativitypreserved. Protein Engineering, 11, 199-204.


H. Shirai, N.Nakajima, J. Higo, A. Kidera and H. Nakamura (1998) Conformational sampling ofCDR-H3 in antibodies by multicanonical molecular dynamics simulation. J. Mol.Biol., 278, 481-496.


T. Mogi, J. Minagawa,T. Hirano, M. Sato-Watanabe, M. Tsubaki, T. Uno, H. Hori, H. Nakamura, Y.Nishimura and Y. Anraku (1998) Substitutions of conserved aromatic amino acidresidues in subunit I perturb the metal centers of the Escherichia coli bo-typeubiquinol oxidase. Biochemistry, 37, 1632-1639.


M. Oda, K. Furukawa,K. Ogata, A. Sarai and H. Nakamura (1998) Thermodynamics of specific andnon-specific DNA binding by the c-Myb DNA-binding domain. J. Mol. Biol., 276,571-590.


M. Oda, K. Furukawa,K. Ogata, A. Sarai, S. Ishii, Y. Nishimura and H. Nakamura (1997) Identificationof indispensable residues for specific DNA-binding in the imperfect tandemrepeats of c-Myb R2R3. Protein Engineering, 10, 1407-1414.


J. Higo, N. Nakajima,H. Shirai, A. Kidera and H. Nakamura (1997) Two-component multicanonical MonteCarlo method for effective conformation sampling. J. Comput. Chem., 18,2086-2092.


N. Nakajima, J. Higo,A. Kidera and H. Nakamura (1997) Flexible docking of a ligand peptide to areceptor protein by multicanonical molecular dyhnamics simulation. Chem. Phys.Lett., 278, 297-301.


A. Heger, J. Higo andH. Nakamura (1997) Model building study of complex structures using NMRchemical shift change information. Proc. Japan Acad., 73B, 109-113.


M. Oda, K. Furukawa, K.Ogata, A. Sarai, S. Ishii, Y. Nishimura and H. Nakamura (1997) Investigation ofthe pyrimidine preference by the c-Myb DNA-binding domain at the initial baseof the consensus sequence. J. Biol. Chem., 272, 17966-17971.


T. Nishizaki, S. Iwai,E. Ohtsuka and H. Nakamura (1997) Solution structure of an RNA•2'-O-methylatedRNA hybrid duplex containing an RNA•DNA hybrid segment at the center.Biochemistry, 36, 2577-2585.


N. Nakajima, H.Nakamura and A. Kidera (1997) Multicanonical ensemble generated by moleculardynamics simulation for enhanced conformational sampling of peptides. J. Phys.Chem., B101, 817-824.


T. Sakuma, H.Kashiwagi, T. Takada and H. Nakamura (1997) Ab initio MO study of thechlorophyll dimer in the photosynthetic reaction center. I. A theoreticaltreatment of the electrostatic field created by the surroudning proteins. Int.J. Quant. Chem., 61, 137-151.


H. Shirai, A. Kideraand H. Nakamura (1996) Structural classification of CDR-H3 in antibodies. FEBSLett., 399, 1-8.


S. Iwai, M. Wakasa, E.Ohtsuka, S. Kanaya, A. Kidera and H. Nakamura (1996) Interaction of the basicprotrusion of Escherichia coli ribonuclease HI with its substrate. J. Mol.Biol., 263, 699-706.


Y. Matsuo, A. Yamada,K. Tsukamoto, H. Tamura, H. Ikezawa, H. Nakamura and K. Nishikawa (1996) Adistinct evolutionary relationships between bacterial sphingomyelinase andmammalian DNase I. Protein Sciecne, 5, 2459-2467.


K. Furukawa, M. Odaand H. Nakamura (1996) A small engineered protein lacks structural uniquenessby increasing the side-chain conformational entropy. Proc. Natl. Acad. Sci.USA, 93, 13583-13588.


H. Nakamura, R.Tanimura and A. Kidera (1996) Side-chain conformations cooperatively restrictedin protein secondary structure II. Side-chain configurational entropies ofa-helices in the folding nuclei. Proc. Japan Acad., 72B, 149-152.


H. Nakamura, R.Tanimura and A. Kidera (1996) Side-chain conformations cooperatively restrictedin protein secondary structure I. A novel method for exhaustive structuresearching. Proc. Japan Acad., 72B, 143-148.


M. Matsuda, S. Ota, R.Tanimura, H. Nakamura, K. Matuoka, T. Takenawa, K. Nagashima and T. Kurata(1996) Interaction between the amino-terminal SH3 domain of CRK and its naturaltarget proteins. J. Biol. Chem., 271, 14468-14472.


T. Nishizaki, S. Iwai,T. Ohkubo, C. Kajima, H. Nakamura, Y. Kyogoku and E. Ohtsuka (1996) Solutionstructures of DNA duplexes containing a DNA/RNA hybrid region,d(GG)r(AGAU)d(GAC)/d(GTCATCTCC) and d(GGAGA)r(UGAC)/d(GTCATCTCC). Biochemistry,35, 4016-4025.


H. Nakamura (1996)Roles of electrostatic interaction in proteins. Quart. Rev. Biophys., 29, 1-90.


K. Ogata, C.Kanei-Ishii, M. Sasaki, H. Hatanaka, A. Nagadoi, M. Enari, H. Nakamura, Y. Nishimura,S. Ishii and A. Sarai (1996) The cavity in the hydrophobic core of MybDNA-binding domain is reseraved for DNA recognition and trans-activation.Nature Struct. Biol., 3, 178-187.


T. Tanaka, A.Nishikawa, Y. Tanaka, H. Nakamura, T. Kodama, T. Imanishi and Doi, T (1996)Synthetic collagen-like domain derived from the macrophage scavenger receptorbinds acetylated low-density lipoprotein in vitro. Protein Eng., 9, 307-313.


A. Nagadoi, S.Morikawa, H. Nakamura, M. Enari, K. Kobayashi, H. Yamamotot, G. Sampei, K.Mizobuchi, M.A. Schumacher, R.G. Brennan and Y. Nishimura (1995) Structuralcomparison of the free and DNA-bound forms of the purine repressor DNA-bindingdomain. Structure, 3, 1217-1224.


S. Morikawa, K. Ogata,A. Sekikawa, A. Sarai, S. Ishii, Y. Nishimura and H. Nakamura (1995)Determination of the nuclear magnetic resonace solution structure of a specificDNA complex of the Myb DNA-binding domain. J. Biomol. NMR, 6, 294-305.


Y. Matsuo, H. Nakamuraand K. Nishikawa (1995) Detection of protein 3D-1D compatibilitycharacterizated by the evaluation of side-chain packing and electrostaticinteractions. J. Biochem., 118, 137-148.


S. Iwai, S. Kataoka,M. Wakasa, E. Ohtsuka and H. Nakamura (1995) Recognition of 2'-hydroxyl groupsby Escherichia coli rigonuclease HI. FEBS Lett., 368, 315-320.


K. Ogata, S. Morikawa,H. Nakamura, H. Hojo, S. Yoshimura, R. Zhang, S. Aimoto, Y. Ametani, Z. Hirata,A. Sarai, S. Ishii and Y. Nishimura (1995) Solution structures of the c-MybDNA-binding domain: Comparison between the free and DNA-complexed forms. NatureStruct. Biol., 2, 309-320.


M. Suzuki and H.Nakamura (1995) Orientation of sperm DNA under a magnetic field. Proc. JapanAcad., 71 Ser.B, 36-38.


H. Shindo, T. Iwaki,R. Ieda, H. Kurumizaka, C. Ueguchi, T. Mizuno, S. Morikawa, H. Nakamura and H.Kuboniwa (1995) Solution structure of the DNA binding domain of anucleoid-associated protein, H-NS, from E. coli. FEBS Lett., 360, 125-131.


R. Tanimura, A. Kideraand H. Nakamura (1994) Determination of protein side-chain packing. ProteinScience, 3, 2358-2365.


I. Fujii, H. Nakamura,T. Sagara and K. Kanematsu (1994) Molecular model building of multiple opioidreceptor subtypes. Med. Cehm. Res., 4, 424-431.


K. Ogata, S. Morikawa,H. Nakamura, A. Sekikawa, T. Inoue, H. Kanai, A. Sarai, S. Ishii and Y.Nishimura (1994) Solution structure of a specific DNA complex of the MybDNA-binding domain with cooperative recognition helices. Cell, 79, 639-648.


M. Ariyoshi, D.G.Vassylyev, H. Iwasaki, H. Nakamura, H. Shinagawa and K. Morikawa (1994) Atomicstructure of the RuvC resolvase: A Holliday junction-specific endonuclease fromE. coli. Cell, 78, 1063-1072.


T. Mogi, H. Nakamuraand Y. Anraku (1994) Molecular structure of a heme-copper redox center of theEscherichia coli ubiquinol oxidase: evidence and model. J. Biochem., 116,471-477.


K. Teraishi, M. Saito,I. Fujii and H. Nakamura (1994) Design of the hapten for the induction ofantibodies catalyzing aldol reaction. J. Mol. Graphics, 12, 282-285.


T. Tanaka, Y. Kuroda,H. Kimura, S. Kidokoro and H. Nakamura (1994) Cooperative deformation of a denovo designed protein. Protein Engineering, 7, 969-976.


H. Nakamura, S.Nagashima and T. Wakabayashi (1994) Electrostatic field around the actinfilament. Synchrotron Radiation in the Biosciences (B. Chance et al. eds.)Oxford Univ. Press, 502-508.


E. Kitakuni, Y.Kuroda, M. Oobatake, T. Tanaka and H. Nakamura (1994) Thermodynamiccharacterization of an artificially designed amphiphilic a-helical peptide containingperiodic prolines: Observations of high thermal stability and colddenaturation. Protein Science, 3, 831-837.


Y. Oda, T. Yamazaki,K. Nagayama, S. Kanaya, Y. Kuroda and H. Nakamura (1994) Individual ionizationconstants of all the carboxyl groups in ribonuclease HI from Escherichia colidetermined by NMR. Biochemistry, 33, 5275-5284.


T. Tanaka, M. Hayashi,H. Kimura, M. Oobatake and H. Nakamura (1994) De novo design and creation of astable artificial protein. Biophys. Chem., 50, 47-61.


Y. Komatsu, M.Koizumi, H. Nakamura and E. Ohtsuka (1994) Loop-size variation to probe a bentstructure of a hairpin ribozyme. J. Am. Chem. Soc., 116, 3692-3696.


T. Tanaka, H. Kimura,M. Hayashi, Y. Fujiyoshi, K-I. Fukuhara and H. Nakamura (1994) Characteristicsof a de novo designed protein. Protein Science, 3, 419-427.


H. Yamada, E. Kanaya,Y. Ueno, M. Ikehara, H. Nakamura and M. Kikuchi (1994) Contribution of ahydrogen bond to the thermal stability of the mutant human lysozyme C77/95S.Bull. Pharm. Bull., 17, 612-616.


Y. Oda, S. Iwai, E.Ohtsuka, M. Ishiwaka, M. Ikehara and H. Nakamura (1993) Binding of nucleicacids to E. coli RNaseHI observed by NMR and CD spectroscopy. Nucl. Acids Res.,21, 4690-4695.


T. Sakuma, T. Takada,H. Kashiwagi, H. and Nakamura (1993) Ab initio MO calculations of thechlorophyll dimer in the photosynthetic reaction center. in 'Computer AidedInnovation of New Materials II ' (M. Doyama, J. Kihara, M. Tanaka and R.Yamamoto eds.) Elsevier Science Publishers B.V.


T. Tanaka, Y. Wada, H.Nakamura, T. Doi, T. Imanishi and T. Kodama (1993) A synthetic model ofcollagen structure taken from bovine macrophage scavenger receptor. FEBS Lett.,334, 272-276.


S. Yajima, Y. Mutot,S. Morikawa, H. Nakamura, S. Yokoyama, H. Masaki and T. Uozumi (1993) Thethree-dimensional structure of the colicin E3 immunity protein by distancegeometry calculation. FEBS Lett., 333, 257-260.


S. Kanaya, M.Oobatake, H. Nakamura and M. Ikehara (1993) pH-dependent themostabilization ofEscherichia coli ribonuclease HI by histidine to alanine substitutions. J.Biotechnology, 28, 117-136.


P.F.W. Stouten, C.Frommel, H. Nakamura and C. Sander (1993) An effective solvation term based onatomic occupancies for use in protein simulations. Molecular Simulation, 10,97-120.


K. Ishikawa, H.Nakamura, K. Morikawa, S. Kimura and S. Kanaya (1993) Cooperative stabilizationof Escherichia coli ribonuclaese HI by insertion of Gly-88b and Gly77 -> Alasubstitution. Biochemistry, 32, 7136-7142.


K. Ishikawa, H. Nakamura,K. Morikawa, S. Kanaya (1993) Stabilization of Escherichia coli ribonuclease HIby cavity filling mutations within a hydrophobic core. Biochemistry, 32,6171-6178.


A.V. Finkelstein andH. Nakamura (1993) Weak points of antiparallel b-sheets; How are they filled upin globular proteins? Protein Engineering, 6, 367-372.


H. Nakamura (1993)Reproduction of correct electrostatic field by charges and dipoles on a closedsurface. J. Mol. Graphics, 43, 30-36.


K. Ishikawa, M.Okumura, K. Katayanagi, S. Kimura, S. Kanaya, H. Nakamura and K. Morikawa(1993) Crystal structure of ribonuclease H from thermus thermophilus HB8refined at 2.8 A resolution. J. Mol. Biol., 230, 529-542.


T. Nakai, A. Kideraand H. Nakamura (1993) Intrinsic nature of the three-dimensional structure ofproteins as determined by distance geometry with good sampling properties. J.Biomol. NMR, 3, 19-40.


T. Doi, K. Higashino,Y. Kurihara, Y. Wada, H. Nakamura, S. Uesugi, T.Imanishi, Y. Kawabe, H.Itakura, Y. Yazaki, A. Matsumoto and T. Kodama (1993) Charged collagenstructure mediates the recognition of negatively charged macromolecules bymacrophage scavenger receptors. J. Biol. Chem., 268, 2126-2133.


K. Ishikawa, S.Kimura, S. Kanaya, K. Morikawa and H. Nakamura (1993) Structural study ofmutants of Escherichia coli ribonuclease HI with enhanced thermostability.Protein Engineering, 6, 85-91.


S. Kimura, S. Kanayaand H. Nakamura (1992) Thermostabilization of Escherichia coli ribonuclease HIby replacing left-handed helical Lys95 with Gly or Asn. J. Biol. Chem., 267,22014-22017.


S. Kimura, H.Nakamura, T. Hashimoto, M. Oobatake and S. Kanaya (1992) Stabilization ofEscherichia coli ribonuclease HI by strategic replacement of amino acidresidues with those from the thermophilic counterpart. J. Biol. Chem., 267,21535-21542.


K. Teraishi, M. Saito,I. Fujii and H. Nakamura (1992) Ab initio structural comparison between thetetrahedral intermediates and the phosphorous-containing analogues in the esterand amide hydrolysis. Tetrahedron lett., 33, 7153-7156.


R. Kuroki, S.Kawakita, H. Nakamura and K. Yutani (1992) Entropic stabilization of a mutanthuman lysozyme induced by calcium binding. Proc. Natl. Acad. Sci. USA, 89,6803-6807.


K. Ogata, H. Hojo, S.Aimoto, T. Nakai, H. Nakamura, A. Sarai, S. Ishii and Y. Nishimura (1992)Solution structure of a DNA-binding unit of Myb: A helix-turn-helix-relatedmotif with conserved tryptophans forming hydrophobic core. Proc. Natl. Acad.Sci. USA, 89, 6428-6432.


T. Nakai, W.Yoshikawa, H. Nakamura and H. Yoshida (1992) The three-dimensional structure ofguanine-specific ribonuclease F1 in solution determined by NMR spectroscopy anddistance geometry. Eur. J. Biochem., 208, 41-51.


S. Kimura, Y. Oda, T.Nakai, K. Katayanagi, E. Kitakuni, C. Nakai, H. Nakamura, M. Ikehara and S.Kanaya (1992) Effect of cavity-modulating mutations on the stability ofEschericia coli ribonuclease HI. Eur. J. Biochem., 206, 337-343.


Y. Oda, H. Nakamura, T.Yamazaki, K. Nagayama, M. Yoshida, S. Kanaya and M. Ikehara (1992) 1H-NMRstudies of deutrated ribonuclease HI selectively labeled with protonated aminoacids. J. Biomol. NMR, 2, 137-147.


E. Kitakuni, T .Horiuchi, Y. Oda, M. Oobatake and H. Nakamura (1992) Design and synthesis of ana-helical peptide containing periodic proline residues. FEBS lett., 298,233-236.


T. Takahashi, H.Nakamura and A. Wada (1992) Electrostatic forces in two lysozymes: Calculationsand measurements of two histidine pKa values. Biopolymers, 32, 897-909.


K. Morikami, T. Nakai,A. Kidera, M. Saito and H. Nakamura (1992) PRESTO:A vectorized molecularmechanics program for biopolymers. Comput & Chem., 16, 243-248.


K. Katayanagi, M.Miyagawa, M. Matsushima, M. Ishikawa, S. Kanaya, H.Nakamura, M. Ikehara, T.Matsuzaki and K. Morikawa (1992) Structural details of ribonuclease H from E.coli as refined to an atomic resolution. J.Mol. Biol., 223, 1029-1052.


C. Sander, G. Vriend,F. Bazan, A. Morovitz, H. Nakamura, L. Ribas, A. V. Finkelstein, A. Lockhart,R. Merkl, L. Jeanne Perry, S. C. Emery, C. Gaboriaud, C. Marks, J. Moult, C.Verlinde, M. Eberhand, A. Elofsson,T.J.P. Hubbard, L.Regan, J.Banks,R.Jappelli, A. Lesk and A. Tramontano (1992) Protein design on computers. Fivenew proteins: Shpilka, Grendel, Fingerclasp, Leather and Aida. Proteins;Struct. Funct. Genet., 12, 105-110.


H. Nakamura, Y. Oda,S. Iwai, H. Inoue, E. Ohtsuka, S. Kanaya, S. Kimura, C. Katsuda, K. Katayanagi,K. Morikawa, H. Miyashiro and M. Ikehara (1991) How does RNase H recognize aDNA-RNA hybrid? Proc. Natl. Acad. Sci. USA, 88, 11535-11539.


Y. Oda, H. Nakamura,S. Kanaya and M. Ikehara (1991) Binding metal ions to E. coli RNase HI observedby 1H-15N heteronuclear 2D NMR. J. Biomol. NMR, 1, 247-255.


K. Nagayama, T.Yamazaki, M. Yoshida, S. Kanaya and H. Nakamura (1991) Ribonuclease H: Fullassignment of backbone proton resonances with heteronuclear 3D NMR and solutionstructure. 'Computational aspects of the study of biological macromolecules bynuclear magnetic resonance spectroscopy' (edt. J. C. Hoch et al.) Plenum Press,New York.


T. Yamazaki, M.Yoshida, S. Kanaya, H. Nakamura and K. Nagayama (1991) Assignments of backbone1H, 13C and 15N resonances and secondary structure of ribonuclease H from E.coli by heteronuclear three-dimensional NMR spectroscopy. Biochemistry, 30,6036-6047.


S. Kanaya, C. Katsuda,S. Kimura, T. Nakai, E. Kitakuni, H. Nakamura,K. Katayanagi, K. Morikawa and M.Ikehara (1991) Stabilization of E. coli ribonuclease H by introduction of anartificial disulphide bond. J. Biol.Chem., 266, 6038-6044.


H. Nakamura (1991)Computer aided design of artificial proteins. Computer Aided Innovation of NewMaterials (M. Doyama, T. Suzuki, J. Kihara and R.Yamamoto Eds.) 417-422,Elsevier.


H. Nakamura, K.Katayanagi, K. Morikawa and M. Ikehara (1991) Structural models of ribonucleaseH domains in reverse transcriptases from retro-viruses. Nuc. Acids Res., 19,1817-1823.


H. Nakamura (1991)Theoretical studies of electrostatic aspects of proteins in 'Recent Advances inBiochemistry' (S.M. Byun et al. eds., Proceedingsof 5'th FAOB congress) 29-42,The Biochemical Society of the Republic of Korea, Seoul.


M. Yoshida, T. Nakai,K. Fukuhara, S. Saitoh, W. Yoshikawa, Y. Kobayashi and H. Nakamura (1990)Three-dimensional structure of an alpha-amylase inhibitor HAIM as determined bynuclear magnetic resonance methods. J. Biochem. (Tokyo), 108, 158-165.


T. Tanaka, K.Fukuhara, H. Nakamura, S. Saito, T. Tanaka, M. Hayashi, Y. Yamamoto, A. Kohara,M. Kikuchi and M. Ikehara (1990) De novo design and the synthesis of TIM barrelproteins. J. Cell Biochem., 14C, 233-233.


S. Kimura, Y. Oda, T.Nakai, K. Katayanagi, H. Nakamura, S. Kanayaand M. Ikehara (1990) J. ProteinChem., 9, 352-352.


T. Sakuma, T. Takada,H. Kashiwagi and H. Nakamura (1990) Ab initio MO calculations of thechlorophyll dimer in the photosynthetic reaction center. Int. J. Quant. Chem.Quant. Biol. Symp., 17, 93-101.


M. Saito and H.Nakamura (1990) Hydration free energy calculations by the acceptance ratiomethod. J. Comput. Chem., 11, 76-81.


R. Kuroki, Y.Taniyama, C. Seko, H. Nakamura, M. Kikuchi and M.Ikehara (1989) Design andcreation of a Ca2+ binding site in human lysozyme to enhance structuralstability. Proc. Natl. Acad. Sci. USA, 86, 6903-6907.


W. Ito, H. Nakamuraand Y. Arata (1989) Protein-protein interactions on the surface ofimmunoglobulin molecules. J. Mol. Graphics, 7, 60-63.


T. Sakamoto, H.Nakamura, H. Uedaira and A. Wada (1989) High-frequency dielectric relaxation ofwater bound to hydrophilic silica gels. J. Phys.Chem., 93, 357-366.


H. Nakamura (1988)Numerical calculations of reaction fields of protein-solvent systems. J. Phys.Soc. Jpn., 57, 3702-3705.


T. Sakamoto, H.Nakamura and A. Wada (1988) Dielectric relaxation measurements of hydratedpowder at subzero temperatures by time-domain reflectometry. Jpn. J. Appl.Phys., 27, 912-916.


H. Nakamura, T.Sakamoto and A. Wada (1988) A theoretical study of the dielectric constant ofprotein. Protein Engineering, 2, 177-183.


H. Nakamura and S.Nishida (1987) Numerical calculations of electrostatic potentials ofprotein-solvent systems by the self consistent boundary method. J. Phys. Soc.Jpn., 56, 1609-1622.


K. Komatsu, S.Nakagawa, H. Umeyama, and H. Nakamura (1987) Electrostatic interaction energyand solvent accessibility in the methotrexate-reduced nicotinamide adeninedinucleotide phosphate-dihydrofolate reductase ternary complex. Chem. Pharm.Bull., 35, 1880-1895.


H. Nakamura and S.Yokoyama (1986) Multi-angular Method for Analysing Molecular Geometry fromNuclear Overhauser Effect Results. J. Mol. Graphics, 4, 161-164.


H. Sato, H. Nakamura,K. Itoh and K. Higashi (1985) Dielectric behaviour of 2-methyl-2-propanol andbutanol isomers in solutions. Chem. Lett. (Chem. Soc. Japan), 1167-1168.


H. Nakamura and A.Wada (1985) Nature of the charge distribution in proteins III. J. Phys. Soc.Jpn., 54, 4047-4052.


A. Wada, H. Nakamura andT. Sakamoto (1985) Nature of the charge distribution in proteins II. J. Phys.Soc. Jpn., 54, 4042-4046.


H. Nakamura, K.Komatsu and H. Umeyama (1985) Electrostatic Complementarities between GuestLigand and Host Enzymes. J. Phys. Soc. Jpn., 54, 3257-3260.


H. Nakamura, K.Komatsu, S. Nakagawa and H. Umeyama (1985) Visualization of enzymes recognizingelectrostatically their ligands and co-factors. J. Mol. Graphics, 3, 2-ll.


K. Komatsu, H.Nakamura, S. Nakagawa and H. Umeyama (1984) Electrostatic forces in theinhibition of dihydrofolate reductase by methotrexate. A field potential study,Chem. Pharm. Bull. Jpn., 32, 3313-3316.


H. Nakamura, M.Kusunoki and N. Yasuoka (1984) A new approach to illustrating electrostaticmolecular surfaces. J. Mol. Graphics, 2, 14-17.


H. Nakamura and K.Okano (1983) Pretransitional phenomena in the isotropic phase of a lyotropicliquid crystal of bacterial virus fd. Phys. Rev. Lett., 50, l86-189.


H. Nakamura and K.Okano (1982) Flow properties of bacteriophage fd and its recombinants. Rep.Prog. Polym. Phys. Jpn. 25, 829-832.


S. Mashimo, H.Nakamura and A. Chiba (1982) Elementary process in polymer chain motion. J.Chem. Phys. , 76, 6342-6345.


H. Nakamura, S.Mashimo and A. Wada (1982) Precise and easy method of TDR to obtain dielectricrelaxtion spectra in GHz region. Jpn. J. Appl. Phys., 21, l022-l024.


H. Nakamura, S.Mashimo and A. Wada (1982) Application of time domain reflectometry covering awide frequency range to the dielectric studyof polymer solutions. Jpn. J. Appl.Phys., 21, 467-474.


H. Nakamura, Y. Naito,Y. Tsuboi, S. Mitaku and K. Okano (1982) Ultrasonic resonance spectrometry withFourier sunthesized pseudorandom noise excitation and its application to alyotropic liquid crystal. Jpn. J. Appl. Phys., 21, l539-l542.


H. Nakamura, K. Okanoand Y. Husimi (1981) Flow properties of concentrated solutions of biologicalsemi-flexible rod-like macromolecule (bacteriophage fd). Rep. Prog. Polym.Phys. Jpn., 24, 621-624.


H. Nakamura and K.Okano (1981) Viscoelastic behavior of fd phage solutions. Biorheology, 18,92-92.


A. Wada and H.Nakamura (1981) Nature of the charge distribution in proteins. Nature, 293,757-758.


H. Nakamura, S.Mashimo and A. Wada (1981) Observation of the side chain motion of polypeptidesin solution by measurement of picosecond dielectric relaxation. Macromolecules,14, l698-1700.


H. Nakamura and A.Wada (1981) Dielectric studies of aqueous solutions of poly(L-glutamic acid).Biopolymers, 20, 2567-2582.


H. Nakamura, Y. Husimiand A. Wada (1981) Time domain measurement of dielectric spectra of aqueouspolyelectrolyte solutions at low frequencies. J. Appl. Phys., 52, 3053-3061.


A. Minakata, T.Shimizu, H. Nakamura and A. Wada (1980) Dielectric dispersion of alternating copolymersof maleic acid. Biophys. Chem., 11, 403-409.


H. Nakamura, Y. Husimiand A. Wada (1977) An application of Fourier synthesis to pseudorandom noisedielectric spectrometer. Jpn. J. Appl. Phys., 16, 2301-2302.


Y. Husimi, H. Nakamuraand A. Wada (1977) Subsecond measurement of dielectric dispersion. Ann. N. Y.Acad. Sci., 303, 90-106.


H. Nakamura, Y.Husimi, G. Parry Jones and A. Wada (1977) Dielectric measurements of solutionsof poly-g-benzyl-L-glutamate using a pseudorandom noise dielectric spectrometer.J. Chem. Soc. Faraday Trans., II 73, ll78-ll90.