Haruki Nakamura

2009
25	EE	Gota Kikugawa, Rossen Apostolov, Narutoshi Kamiya, Makoto Taiji, Ryutaro Himeno, Haruki Nakamura, Yasushige Yonezawa: Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems. Journal of Computational Chemistry 30(1): 110-118 (2009)
2008
24	EE	Daron M. Standley, Akira R. Kinjo, Kengo Kinoshita, Haruki Nakamura: Protein structure databases with new web services for structural biology and biomedical research. Briefings in Bioinformatics 9(4): 276-285 (2008)
23	EE	Kim Henrick, Zukang Feng, Wolfgang Bluhm, Dimitris Dimitropoulos, Jurgen F. Doreleijers, Shuchismita Dutta, Judith L. Flippen-Anderson, John M. C. Ionides, Chisa Kamada, Eugene Krissinel, Catherine L. Lawson, John L. Markley, Haruki Nakamura, Richard Newman, Yukiko Shimizu, Jawahar Swaminathan, Sameer Velankar, Jeramia Ory, Eldon L. Ulrich, Wim Vranken, John D. Westbrook, Reiko Yamashita, Huanwang Yang, Jasmine Young, Muhammed Yousufuddin, Helen M. Berman: Remediation of the protein data bank archive. Nucleic Acids Research 36(Database-Issue): 426-433 (2008)
2007
22	EE	Susumu Date, Takahito Tashiro, Kazunori Nozaki, Haruki Nakamura, Saburo Sakoda, Shinji Shimojo: A Grid-Ready Clinical Database for Parkinson's Disease Research and Diagnosis. CBMS 2007: 483-488
21	EE	Helen M. Berman, Kim Henrick, Haruki Nakamura, John L. Markley: The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Research 35(Database-Issue): 301-303 (2007)
20	EE	Kengo Kinoshita, Yoichi Murakami, Haruki Nakamura: eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape. Nucleic Acids Research 35(Web-Server-Issue): 398-402 (2007)
2006
19	EE	David Abramson, Amanda Lynch, Hiroshi Takemiya, Yusuke Tanimura, Susumu Date, Haruki Nakamura, Karpjoo Jeong, Suntae Hwang, Ji Zhu, Zhonghua Lu, Céline Amoreira, Kim Baldridge, Hurng-Chun Lee, Chi-Wei Wang, Horng-Liang Shih, Tomas E. Molina, Wilfred W. Li, Peter W. Arzberger: Deploying Scientific Applications to the PRAGMA Grid Testbed: Strategies and Lessons. CCGRID 2006: 241-248
18	EE	Yuko Tsuchiya, Kengo Kinoshita, Nobutoshi Ito, Haruki Nakamura: PreBI: prediction of biological interfaces of proteins in crystals. Nucleic Acids Research 34(Web-Server-Issue): 20-24 (2006)
2005
17	EE	Haruki Nakamura: Protein informatics towards integration of data grid and computing grid. APBC 2005: 359-362
16	EE	Ashwini Patil, Haruki Nakamura: Filtering high-throughput protein-protein interaction data using a combination of genomic features. BMC Bioinformatics 6: 100 (2005)
15	EE	Daron M. Standley, Hiroyuki Toh, Haruki Nakamura: GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures. BMC Bioinformatics 6: 221 (2005)
14	EE	John D. Westbrook, Nobutoshi Ito, Haruki Nakamura, Kim Henrick, Helen M. Berman: PDBML: the representation of archival macromolecular structure data in XML. Bioinformatics 21(7): 988-992 (2005)
13	EE	Yuko Tsuchiya, Kengo Kinoshita, Haruki Nakamura: PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces. Bioinformatics 21(8): 1721-1723 (2005)
2004
12	EE	Kengo Kinoshita, Haruki Nakamura: eF-site and PDBjViewer: database and viewer for protein functional sites. Bioinformatics 20(8): 1329-1330 (2004)
11	EE	Haruki Nakamura, Susumu Date, Hideo Matsuda, Shinji Shimojo: A Challenge towards Next-Generation Research Infrastructure for Advanced Life Science. New Generation Comput. 22(2): (2004)
2003
10		Youhei Kawaguchi, Yoshikazu Kaneta, Takenao Ohkawa, Haruki Nakamura: Information Extraction from Semi-Structured Data in the Protein Data Bank by Induction of a Data Description Pattern. METMBS 2003: 94-99
9	EE	Kazuyoshi Ikeda, Oxana V. Galzitskaya, Haruki Nakamura, Junichi Higo: beta-Hairpins, alpha-helices, and the intermediates among the secondary structures in the energy landscape of a peptide from a distal beta-hairpin of SH3 domain. Journal of Computational Chemistry 24(3): 310-318 (2003)
2002
8		Tadasuke Nakagawa, Takanori Tanaka, Takenao Ohkawa, Haruki Nakamura: A Filtering Method for High-Speed Retrieval of Similar Active Sites. JCIS 2002: 1207-1212
7		Yoshikazu Kaneta, Norimasa Shoji, Takenao Ohkawa, Haruki Nakamura: A Method of Comparing Protein Molecular Surface Based on Normal Vectors with Attributes and Its Application to Function Identification. JCIS 2002: 1213-1218
6	EE	Yoshikazu Kaneta, Norimasa Shoji, Takenao Ohkawa, Haruki Nakamura: A method of comparing protein molecular surface based on normal vectors with attributes and its application to function identification. Inf. Sci. 146(1-4): 41-54 (2002)
5	EE	Tadasuke Nakagawa, Takanori Tanaka, Takenao Ohkawa, Haruki Nakamura: A filtering method for high-speed retrieval of similar active sites. Inf. Sci. 146(1-4): 55-65 (2002)
4	EE	Satoshi Ono, Masataka Kuroda, Junichi Higo, Nobuyuki Nakajima, Haruki Nakamura: Calibration of force-field dependency in free energy landscapes of peptide conformations by quantum chemical calculations. Journal of Computational Chemistry 23(4): 470-476 (2002)
2001
3	EE	Junichi Higo, Yasunobu Sugimoto, Katsuzo Wakabayashi, Haruki Nakamura: Collective motions of myosin head derived from backbone molecular dynamics and combination with X-ray solution scattering data. Journal of Computational Chemistry 22(16): 1983-1994 (2001)
2000
2	EE	Satoshi Ono, Nobuyuki Nakajima, Junichi Higo, Haruki Nakamura: Peptide free-energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95. Journal of Computational Chemistry 21(9): 748-762 (2000)
1992
1	EE	Kenji Morikami, Takahisa Nakai, Akinori Kidera, Minoru Saito, Haruki Nakamura: Presto(protein Engineering Simulator): A Vectorized Molecular Mechanics Program for Biopolymers. Computers & Chemistry 16(3): 243-248 (1992)

Coauthor Index

1	David Abramson	[19]
2	Céline Amoreira	[19]
3	Rossen Apostolov	[25]
4	Peter W. Arzberger	[19]
5	Kim Baldridge	[19]
6	Helen M. Berman	[14] [21] [23]
7	Wolfgang Bluhm	[23]
8	Susumu Date	[11] [19] [22]
9	Dimitris Dimitropoulos	[23]
10	Jurgen F. Doreleijers	[23]
11	Shuchismita Dutta	[23]
12	Zukang Feng	[23]
13	Judith L. Flippen-Anderson	[23]
14	Oxana V. Galzitskaya	[9]
15	Kim Henrick	[14] [21] [23]
16	Junichi Higo	[2] [3] [4] [9]
17	Ryutaro Himeno	[25]
18	Suntae Hwang	[19]
19	Kazuyoshi Ikeda	[9]
20	John M. C. Ionides	[23]
21	Nobutoshi Ito	[14] [18]
22	Karpjoo Jeong	[19]
23	Chisa Kamada	[23]
24	Narutoshi Kamiya	[25]
25	Yoshikazu Kaneta	[6] [7] [10]
26	Youhei Kawaguchi	[10]
27	Akinori Kidera	[1]
28	Gota Kikugawa	[25]
29	Akira R. Kinjo	[24]
30	Kengo Kinoshita	[12] [13] [18] [20] [24]
31	Eugene Krissinel	[23]
32	Masataka Kuroda	[4]
33	Catherine L. Lawson	[23]
34	Hurng-Chun Lee	[19]
35	Wilfred W. Li	[19]
36	Zhonghua Lu	[19]
37	Amanda Lynch	[19]
38	John L. Markley	[21] [23]
39	Hideo Matsuda	[11]
40	Tomas E. Molina	[19]
41	Kenji Morikami	[1]
42	Yoichi Murakami	[20]
43	Tadasuke Nakagawa	[5] [8]
44	Takahisa Nakai	[1]
45	Nobuyuki Nakajima	[2] [4]
46	Richard Newman	[23]
47	Kazunori Nozaki	[22]
48	Takenao Ohkawa	[5] [6] [7] [8] [10]
49	Satoshi Ono	[2] [4]
50	Jeramia Ory	[23]
51	Ashwini Patil	[16]
52	Minoru Saito	[1]
53	Saburo Sakoda	[22]
54	Horng-Liang Shih	[19]
55	Yukiko Shimizu	[23]
56	Shinji Shimojo	[11] [22]
57	Norimasa Shoji	[6] [7]
58	Daron M. Standley	[15] [24]
59	Yasunobu Sugimoto	[3]
60	Jawahar Swaminathan	[23]
61	Makoto Taiji	[25]
62	Hiroshi Takemiya	[19]
63	Takanori Tanaka	[5] [8]
64	Yusuke Tanimura	[19]
65	Takahito Tashiro	[22]
66	Hiroyuki Toh	[15]
67	Yuko Tsuchiya	[13] [18]
68	Eldon L. Ulrich	[23]
69	Sameer Velankar	[23]
70	Wim Vranken	[23]
71	Katsuzo Wakabayashi	[3]
72	Chi-Wei Wang	[19]
73	John D. Westbrook	[14] [23]
74	Reiko Yamashita	[23]
75	Huanwang Yang	[23]
76	Yasushige Yonezawa	[25]
77	Jasmine Young	[23]
78	Muhammed Yousufuddin	[23]
79	Ji Zhu	[19]

Colors in the list of coauthors