論文

1. Protein Data Bank Japan (PDBj): Maintaining a structural data archive and Resource Description Framework format，Kinjo AR, Suzuki H, Yamashita R, Ikegawa Y, Kudo T, Igarashi R, Kengaku Y, Cho H, Standley DM, Nakagawa A, Nakamura H，Nucleic Acids Research，40:D453-D460，2012年01月，http://dx.doi.org/10.1093/nar/gkr811，学術論文

2. A Free-Energy Landscape for Coupled Folding and Binding of an Intrinsically Disordered Protein in Explicit Solvent from Detailed All-Atom Computations，Higo Junichi, Nishimura Yoshifumi, Nakamura Haruki，J. Ame. Chem. Soc.，133, 10448-10458，2011年05月，学術論文

3. Molecular dynamics scheme for precise estimation of electrostatic interaction via zero-dipole summation principle.，Fukuda Ikuo, Yonezawa Yasushige, Nakamura Haruki，J. Chem. Phys.，134, 164107，2011年04月，学術論文

4. 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.，Yasushige Yonezawa, Kazuto Nakata, Kota Sakakura, Toshikazu Takada, Haruki Nakamura，J. Am. Chem. Soc.，131 (12) 4535-4540，2009年03月，学術論文

5. Comprehensive structural classification of ligand binding motifs in proteins，Akira R. Kinjo, Haruki Nakamura，Structure，17 (2), 234-246，2009年02月，学術論文

6. 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.，Kamiya, N., Yonezawa, Y., Nakamura, H., Higo, J.，PROTEINS，70 (1)，2008年01月，学術論文

7. eF-seek: Prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape.，Kinoshita, K., Murakami, Y., Nakamura, H.，Nucleic Acids Research，35，2007年06月，学術論文

8. Docking of protein molecular surfaces with evolutionary trace analysis.，Kanamori, E., Murakami, Y., Tsuchiya, Y., Standley, D. M., Nakamura, H., Kinoshita, K.，PROTEINS，69 (4)，2007年06月，学術論文

9. 蛋白質構造情報から蛋白質機能情報へ，中村春木，2007年02月，会議報告/口頭発表

10. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data.，Berman, H., Henrick, K., Nakamura, H., Markley, J. L.，Nucleic Acids Research，35，2007年01月，学術論文

11. Structural Features of Hubs in Protein-Protein Interaction Networks，Nakamura, H.，2007年01月，国際会議（proceedingsあり）

12. Molecular Dynamics Simulation Study on Water Associated with π-electrons of Benzene by using QM/MM Potential.，Yonezawa, Y., Nakata, K., Takada, T., Nakamura, H.，Chemical Physics Letters，428 (1-3)，2006年10月，学術論文

13. PDBML: Impact of the new PDB format and its application to GRID，Nakamura, H.，2006年05月，国際会議（proceedingsあり）

14. Disordered domains and high surface charge confer hubs with the ability to interact with multiple proteins in interaction networks.，Patil, A., Nakamura, H.，FEBS Letters，580 (8)，2006年04月，学術論文

15. Classification of chemical compounds by protein-compound docking for use in designing a focused library.，Fukunishi, Y., Mikami, Y., Takedomi, K., Yamanouchi, M., Shima, H., Nakamura, H.，Journal of Medicinary Chemistry，49 (2)，2006年02月，学術論文

16. PDBML: the XML-based database and its Applications.，Nakamura, H.，2005年08月，国際会議（proceedingsあり）

17. Announcing the worldwide Protein Data Bank，Helen Berman, Kim Henrick, Haruki Nakamura，Nature Structural Biology，2003年12月，解説・総説

18. Identification of protein biochemical functions by similarity search using the molecular surface database, eF-site.，Kengo Kinoshita, Haruki Nakamura，Protein Science，2003年08月，学術論文

19. Protein informatics towards function identification.，Kengo Kinoshita, Haruki Nakamura，Current Opininion in Structural Biology，2003年06月，解説・総説

20. Free energy landscapes of peptides by enhanced conformational sampling，Nobuyuki Nakajima, Junichi Higo, Akinori Kidera, Haruki Nakamura，Journal of Molecular Biology，2000年02月，学術論文