Haruki Nakamura

75 papers B 3Journal 63Unranked 9

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Correction: Phenology analysis for trait prediction using UAVs in a MAGIC rice population with different transplanting protocols. Frontiers Artif. Intell. Shoji Taniguchi, Toshihiro Sakamoto, Haruki Nakamura, Yasunori Nonoue, Di Guan, Akari Fukuda, Hirofumi Fukuda, Kaede C. Wada, Takuro Ishii, Jun-Ichi Yonemaru, Daisuke Ogawa
2024	J	`jnl`	Phenology analysis for trait prediction using UAVs in a MAGIC rice population with different transplanting protocols. Frontiers Artif. Intell. Shoji Taniguchi, Toshihiro Sakamoto, Haruki Nakamura, Yasunori Nonoue, Di Guan, Akari Fukuda, Hirofumi Fukuda, Kaede C. Wada, Takuro Ishii, Jun-Ichi Yonemaru, Daisuke Ogawa
2020	J	`jnl`	Molecular Interaction Mechanism of a 14-3-3 Protein with a Phosphorylated Peptide Elucidated by Enhanced Conformational Sampling. J. Chem. Inf. Model. Junichi Higo, Takeshi Kawabata, Ayumi Kusaka, Kota Kasahara, Narutoshi Kamiya, Ikuo Fukuda, Kentaro Mori, Yutaka Hata, Yoshifumi Fukunishi, Haruki Nakamura
2019	J	`jnl`	Hydrogen bond donors and acceptors are generally depolarized in α-helices as revealed by a molecular tailoring approach. J. Comput. Chem. Hiroko X. Kondo, Ayumi Kusaka, Colin K. Kitakawa, Jinta Onari, Shusuke Yamanaka, Haruki Nakamura, Yu Takano
2019	J	`jnl`	Multidimensional virtual-system coupled canonical molecular dynamics to compute free-energy landscapes of peptide multimer assembly. J. Comput. Chem. Tomonori Hayami, Junichi Higo, Haruki Nakamura, Kota Kasahara
2018	—	`conf`	Construction of Haptic Experience Sharing Platform. UbiComp/ISWC Adjunct Haruki Nakamura, Daiya Kato, Roshan Lalintha Peiris, Kouta Minamizawa, Yutaka Kamamoto, Junji Watanabe
2018	J	`jnl`	Density functional study of porphyrin distortion effects on redox potential of heme. J. Comput. Chem. Yasuhiro Imada, Haruki Nakamura, Yu Takano
2018	—	`conf`	HaptI/O: Physical I/O Node over the Internet. EuroHaptics (2) Satoshi Matsuzono, Haruki Nakamura, Daiya Kato, Roshan Lalintha Peiris, Kouta Minamizawa
2018	J	`jnl`	Molecular dynamics coupled with a virtual system for effective conformational sampling. J. Comput. Chem. Tomonori Hayami, Kota Kasahara, Haruki Nakamura, Junichi Higo
2018	J	`jnl`	Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. Database J. Biol. Databases Curation Jasmine Young, John D. Westbrook, Zukang Feng, Ezra Peisach, Irina Persikova, Raul Sala, Sanchayita Sen, John M. Berrisford, Jawahar Swaminathan, Thomas J. Oldfield, Aleksandras Gutmanas, Reiko Igarashi, David R. Armstrong, Kumaran Baskaran, Li Chen, Minyu Chen, Alice R. Clark, Luigi Di Costanzo, Dimitris Dimitropoulos, Guanghua Gao, Sutapa Ghosh, Swanand P. Gore, Vladimir Guranovic, Pieter M. S. Hendrickx, Brian P. Hudson, Yasuyo Ikegawa, Yumiko Kengaku, Catherine L. Lawson, Yuhe Liang, Lora Mak, Abhik Mukhopadhyay, Buvaneswari Coimbatore Narayanan, Kayoko Nishiyama, Ardan Patwardhan, Gaurav Sahni, Eduardo Sanz-García, Junko Sato, Monica Sekharan, Chenghua Shao, Oliver S. Smart, Lihua Tan, Glen van Ginkel, Huanwang Yang, Marina Zhuravleva, John L. Markley, Haruki Nakamura, Genji Kurisu, Gerard J. Kleywegt, Sameer Velankar, Helen M. Berman, Stephen K. Burley
2017	—	`conf`	HaptI/O: Physical Node for the Internet of Haptics. UIST (Adjunct Volume) Satoshi Matsuzono, Haruki Nakamura, Daiya Kato, Roshan Lalintha Peiris, Kouta Minamizawa
2017	J	`jnl`	Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures. Nucleic Acids Res. Akira R. Kinjo, Gert-Jan Bekker, Hirofumi Suzuki, Yuko Tsuchiya, Takeshi Kawabata, Yasuyo Ikegawa, Haruki Nakamura
2016	—	`conf`	A Finger Sensor for Sharing Visual and Tactile Experience. AsiaHaptics Haruki Nakamura, Nobuhisa Hanamitsu, Junichi Kanebako, Kouta Minamizawa
2016	J	`jnl`	Development of massive multilevel molecular dynamics simulation program, platypus (PLATform for dYnamic protein unified simulation), for the elucidation of protein functions. J. Comput. Chem. Yu Takano, Kazuto Nakata, Yasushige Yonezawa, Haruki Nakamura
2016	J	`jnl`	Model Building of Antibody-Antigen Complex Structures Using GBSA Scores. J. Chem. Inf. Model. Noriko Shimba, Narutoshi Kamiya, Haruki Nakamura
2016	J	`jnl`	Molmil: a molecular viewer for the PDB and beyond. J. Cheminformatics Gert-Jan Bekker, Haruki Nakamura, Akira R. Kinjo
2016	J	`jnl`	Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB. Bioinform. Hirofumi Suzuki, Takeshi Kawabata, Haruki Nakamura
2016	J	`jnl`	Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins. J. Biomed. Semant. Masashi Yokochi, Naohiro Kobayashi, Eldon L. Ulrich, Akira R. Kinjo, Takeshi Iwata, Yannis E. Ioannidis, Miron Livny, John L. Markley, Haruki Nakamura, Chojiro Kojima, Toshimichi Fujiwara
2016	J	`jnl`	Variation of free-energy landscape of the p53 C-terminal domain induced by acetylation: Enhanced conformational sampling. J. Comput. Chem. Shinji Iida, Tadaaki Mashimo, Takashi Kurosawa, Hironobu Hojo, Hiroya Muta, Yuji Goto, Yoshifumi Fukunishi, Haruki Nakamura, Junichi Higo
2016	J	`jnl`	Web-based Molecular Graphics (NII Shonan Meeting 2016-12). NII Shonan Meet. Rep. Andrea Schafferhans, Seán I. O'Donoghue, Haruki Nakamura
2016	J	`jnl`	mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories. Bioinform. Kota Kasahara, Neetha Mohan, Ikuo Fukuda, Haruki Nakamura
2015	—	`conf`	A(touch)ment: a smartphone extension for instantly sharing visual and tactile experience. AH Haruki Nakamura, Nobuhisa Hanamitsu, Kouta Minamizawa
2015	J	`jnl`	Computational Study of Drug Binding Affinity to Influenza A Neuraminidase Using Smooth Reaction Path Generation (SRPG) Method. J. Chem. Inf. Model. Hung Nguyen, Tien Tran, Yoshifumi Fukunishi, Junichi Higo, Haruki Nakamura, Ly Le
2015	—	`conf`	Twech: a mobile platform to search and share visuo-tactile experiences. SIGGRAPH Asia Mobile Graphics and Interactive Applications Nobuhisa Hanamitsu, Haruki Nakamura, Masashi Nakatani, Kouta Minamizawa
2015	J	`jnl`	Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking. J. Comput. Chem. Junichi Higo, Bhaskar DasGupta, Tadaaki Mashimo, Kota Kasahara, Yoshifumi Fukunishi, Haruki Nakamura
2014	J	`jnl`	3D Flexible Alignment Using 2D Maximum Common Substructure: Dependence of Prediction Accuracy on Target-Reference Chemical Similarity. J. Chem. Inf. Model. Takeshi Kawabata, Haruki Nakamura
2014	J	`jnl`	Kotai Antibody Builder: automated high-resolution structural modeling of antibodies. Bioinform. Kazuo Yamashita, Kazuyoshi Ikeda, Karlou Mar Amada, Shide Liang, Yuko Tsuchiya, Haruki Nakamura, Hiroki Shirai, Daron M. Standley
2014	J	`jnl`	Prediction of Synthetic Accessibility Based on Commercially Available Compound Databases. J. Chem. Inf. Model. Yoshifumi Fukunishi, Takashi Kurosawa, Yoshiaki Mikami, Haruki Nakamura
2014	J	`jnl`	The Protein Data Bank archive as an open data resource. J. Comput. Aided Mol. Des. Helen M. Berman, Gerard J. Kleywegt, Haruki Nakamura, John L. Markley
2013	J	`jnl`	Protein Experimental Information Management System (PREIMS) Based on Ontology: Development and Applications. Inf. Media Technol. Junko Sato, Kouji Kozaki, Susumu Handa, Takashi Ikeda, Ryotaro Saka, Kohei Tomizuka, Yugo Nishiyama, Toshiyuki Okumura, Shinichi Hirai, Tadashi Ohno, Mamoru Ohta, Susumu Date, Haruki Nakamura
2012	J	`jnl`	Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. Nucleic Acids Res. Akira R. Kinjo, Hirofumi Suzuki, Reiko Yamashita, Yasuyo Ikegawa, Takahiro Kudou, Reiko Igarashi, Yumiko Kengaku, Hasumi Cho, Daron M. Standley, Atsushi Nakagawa, Haruki Nakamura
2011	J	`jnl`	Definition of Drug-Likeness for Compound Affinity. J. Chem. Inf. Model. Yoshifumi Fukunishi, Haruki Nakamura
2011	J	`jnl`	HitPredict: a database of quality assessed protein-protein interactions in nine species. Nucleic Acids Res. Ashwini Patil, Kenta Nakai, Haruki Nakamura
2011	J	`jnl`	Selection of In Silico Drug Screening Results for G-Protein-Coupled Receptors by Using Universal Active Probes. J. Chem. Inf. Model. Mitsuhito Wada, Eiji Kanamori, Haruki Nakamura, Yoshifumi Fukunishi
2011	J	`jnl`	Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water. J. Comput. Chem. Jinzen Ikebe, Koji Umezawa, Narutoshi Kamiya, Takanori Sugihara, Yasushige Yonezawa, Yu Takano, Haruki Nakamura, Junichi Higo
2010	J	`jnl`	Electronic structures of heme J. Comput. Chem. Yu Takano, Haruki Nakamura
2010	J	`jnl`	PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan. Database J. Biol. Databases Curation Akira R. Kinjo, Reiko Yamashita, Haruki Nakamura
2010	J	`jnl`	PiRaNhA: a server for the computational prediction of RNA-binding residues in protein sequences. Nucleic Acids Res. Yoichi Murakami, Ruth V. Spriggs, Haruki Nakamura, Susan Jones
2010	J	`jnl`	Selection of In Silico Drug Screening Results by Using Universal Active Probes (UAPs). J. Chem. Inf. Model. Yoshifumi Fukunishi, Kazuki Ohno, Masaya Orita, Haruki Nakamura
2009	J	`jnl`	A Grid-aware Access Control Mechanism in a Clinical Database for Parkinson's Disease Research and Diagnosis. Inf. Media Technol. Susumu Date, Kazunori Nozaki, Haruki Nakamura, Saburo Sakoda, Shinji Shimojo
2009	J	`jnl`	Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems. J. Comput. Chem. Gota Kikugawa, Rossen Apostolov, Narutoshi Kamiya, Makoto Taiji, Ryutaro Himeno, Haruki Nakamura, Yasushige Yonezawa
2009	J	`jnl`	In Silico Fragment Screening by Replica Generation (FSRG) Method for Fragment-Based Drug Design. J. Chem. Inf. Model. Yoshifumi Fukunishi, Tadaaki Mashimo, Masaya Orita, Kazuki Ohno, Haruki Nakamura
2009	J	`jnl`	Numerical examination of the extended phase-space volume-preserving integrator by the Nosé-Hoover molecular dynamics equations. J. Comput. Chem. Séverine Queyroy, Haruki Nakamura, Ikuo Fukuda
2009	J	`jnl`	Protein function annotation from sequence: prediction of residues interacting with RNA. Bioinform. Ruth V. Spriggs, Yoichi Murakami, Haruki Nakamura, Susan Jones
2009	J	`jnl`	Protein-Ligand Binding Free Energy Calculation by the Smooth Reaction Path Generation (SRPG) Method. J. Chem. Inf. Model. Yoshifumi Fukunishi, Daisuke Mitomo, Haruki Nakamura
2008	J	`jnl`	Improvement of Protein-Compound Docking Scores by Using Amino-Acid Sequence Similarities of Proteins. J. Chem. Inf. Model. Yoshifumi Fukunishi, Haruki Nakamura
2008	J	`jnl`	Protein structure databases with new web services for structural biology and biomedical research. Briefings Bioinform. Daron M. Standley, Akira R. Kinjo, Kengo Kinoshita, Haruki Nakamura
2008	J	`jnl`	Remediation of the protein data bank archive. Nucleic Acids Res. 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 H. Newman, Yukiko Shimizu, Jawahar Swaminathan, Sameer Velankar, Jeramia Ory, Eldon L. Ulrich, Wim F. Vranken, John D. Westbrook, Reiko Yamashita, Huanwang Yang, Jasmine Young, Muhammed Yousufuddin, Helen M. Berman
2007	B	`conf`	A Grid-Ready Clinical Database for Parkinson's Disease Research and Diagnosis. CBMS Susumu Date, Takahito Tashiro, Kazunori Nozaki, Haruki Nakamura, Saburo Sakoda, Shinji Shimojo
2007	J	`jnl`	ASH structure alignment package: Sensitivity and selectivity in domain classification. BMC Bioinform. Daron M. Standley, Hiroyuki Toh, Haruki Nakamura
2007	J	`jnl`	The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res. Helen M. Berman, Kim Henrick, Haruki Nakamura, John L. Markley
2007	J	`jnl`	eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape. Nucleic Acids Res. Kengo Kinoshita, Yoichi Murakami, Haruki Nakamura
2006	J	`jnl`	A Virtual Active Compound Produced from the Negative Image of a Ligand-binding Pocket, and its Application to in-silico Drug Screening. J. Comput. Aided Mol. Des. Yoshifumi Fukunishi, Satoru Kubota, Chisato Kanai, Haruki Nakamura
2006	J	`jnl`	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) Ligands. J. Chem. Inf. Model. Yoshifumi Fukunishi, Shinichi Hojo, Haruki Nakamura
2006	B	`conf`	Deploying Scientific Applications to the PRAGMA Grid Testbed: Strategies and Lessons. CCGRID David Abramson, Amanda Lynch, Hiroshi Takemiya, Yusuke Tanimura, Susumu Date, Haruki Nakamura, Karpjoo Jeong, Suntae Hwang, Ji Zhu, Zhonghua Lu, Céline Amoreira, Kim K. Baldridge, Hurng-Chun Lee, Chi-Wei Wang, Horng-Liang Shih, Tomas E. Molina, Wilfred W. Li, Peter W. Arzberger
2006	J	`jnl`	Noise Reduction Method for Molecular Interaction Energy: Application to in Silico Drug Screening and in Silico Target Protein Screening. J. Chem. Inf. Model. Yoshifumi Fukunishi, Satoru Kubota, Haruki Nakamura
2006	J	`jnl`	PreBI: prediction of biological interfaces of proteins in crystals. Nucleic Acids Res. Yuko Tsuchiya, Kengo Kinoshita, Nobutoshi Ito, Haruki Nakamura
2005	J	`jnl`	Filtering high-throughput protein-protein interaction data using a combination of genomic features. BMC Bioinform. Ashwini Patil, Haruki Nakamura
2005	J	`jnl`	GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures. BMC Bioinform. Daron M. Standley, Hiroyuki Toh, Haruki Nakamura
2005	J	`jnl`	PDBML: the representation of archival macromolecular structure data in XML. Bioinform. John D. Westbrook, Nobutoshi Ito, Haruki Nakamura, Kim Henrick, Helen M. Berman
2005	J	`jnl`	PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces. Bioinform. Yuko Tsuchiya, Kengo Kinoshita, Haruki Nakamura
2005	B	`conf`	Protein informatics towards integration of data grid and computing grid. APBC Haruki Nakamura
2004	J	`jnl`	A Challenge towards Next-Generation Research Infrastructure for Advanced Life Science. New Gener. Comput. Haruki Nakamura, Susumu Date, Hideo Matsuda, Shinji Shimojo
2004	J	`jnl`	A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor. J. Comput. Chem. Rie Tatsumi, Yoshifumi Fukunishi, Haruki Nakamura
2004	J	`jnl`	eF-site and PDBjViewer: database and viewer for protein functional sites. Bioinform. Kengo Kinoshita, Haruki Nakamura
2003	—	`conf`	Information Extraction from Semi-Structured Data in the Protein Data Bank by Induction of a Data Description Pattern. METMBS Youhei Kawaguchi, Yoshikazu Kaneta, Takenao Ohkawa, Haruki Nakamura
2003	J	`jnl`	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. J. Comput. Chem. Kazuyoshi Ikeda, Oxana V. Galzitskaya, Haruki Nakamura, Junichi Higo
2002	—	`conf`	A Filtering Method for High-Speed Retrieval of Similar Active Sites. JCIS Tadasuke Nakagawa, Takanori Tanaka, Takenao Ohkawa, Haruki Nakamura
2002	—	`conf`	A Method of Comparing Protein Molecular Surface Based on Normal Vectors with Attributes and Its Application to Function Identification. JCIS Yoshikazu Kaneta, Norimasa Shoji, Takenao Ohkawa, Haruki Nakamura
2002	J	`jnl`	A filtering method for high-speed retrieval of similar active sites. Inf. Sci. Tadasuke Nakagawa, Takanori Tanaka, Takenao Ohkawa, Haruki Nakamura
2002	J	`jnl`	A method of comparing protein molecular surface based on normal vectors with attributes and its application to function identification. Inf. Sci. Yoshikazu Kaneta, Norimasa Shoji, Takenao Ohkawa, Haruki Nakamura
2002	J	`jnl`	Calibration of force-field dependency in free energy landscapes of peptide conformations by quantum chemical calculations. J. Comput. Chem. Satoshi Ono, Masataka Kuroda, Junichi Higo, Nobuyuki Nakajima, Haruki Nakamura
2001	J	`jnl`	Collective motions of myosin head derived from backbone molecular dynamics and combination with X-ray solution scattering data. J. Comput. Chem. Junichi Higo, Yasunobu Sugimoto, Katsuzo Wakabayashi, Haruki Nakamura
2000	J	`jnl`	Peptide free-energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95. J. Comput. Chem. Satoshi Ono, Nobuyuki Nakajima, Junichi Higo, Haruki Nakamura
1992	J	`jnl`	Presto(protein Engineering Simulator): A Vectorized Molecular Mechanics Program for Biopolymers. Comput. Chem. Kenji Morikami, Takahisa Nakai, Akinori Kidera, Minoru Saito, Haruki Nakamura