Haruki Nakamura

Publication Activity (10 Years)

Years Active: 1992-2020
Publications (10 Years): 19

Top Topics

False Dismissal

Protein Folding

Energy Landscape

Molecular Structure

Top Venues

J. Comput. Chem.

J. Chem. Inf. Model.

J. Cheminformatics

Publications

Junichi Higo, Takeshi Kawabata, Ayumi Kusaka, Kota Kasahara, Narutoshi Kamiya, Ikuo Fukuda, Kentaro Mori, Yutaka Hata, Yoshifumi Fukunishi, Haruki Nakamura
Molecular Interaction Mechanism of a 14-3-3 Protein with a Phosphorylated Peptide Elucidated by Enhanced Conformational Sampling. J. Chem. Inf. Model. 60 (10) (2020)
Tomonori Hayami, Junichi Higo, Haruki Nakamura, Kota Kasahara
Multidimensional virtual-system coupled canonical molecular dynamics to compute free-energy landscapes of peptide multimer assembly. J. Comput. Chem. 40 (28) (2019)
Hiroko X. Kondo, Ayumi Kusaka, Colin K. Kitakawa, Jinta Onari, Shusuke Yamanaka, Haruki Nakamura, Yu Takano
Hydrogen bond donors and acceptors are generally depolarized in α-helices as revealed by a molecular tailoring approach. J. Comput. Chem. 40 (23) (2019)
Haruki Nakamura, Daiya Kato, Roshan Lalintha Peiris, Kouta Minamizawa, Yutaka Kamamoto, Junji Watanabe
Construction of Haptic Experience Sharing Platform. UbiComp/ISWC Adjunct (2018)
Yasuhiro Imada, Haruki Nakamura, Yu Takano
Density functional study of porphyrin distortion effects on redox potential of heme. J. Comput. Chem. 39 (3) (2018)
Satoshi Matsuzono, Haruki Nakamura, Daiya Kato, Roshan Lalintha Peiris, Kouta Minamizawa
HaptI/O: Physical I/O Node over the Internet. EuroHaptics (2) (2018)
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
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. Database J. Biol. Databases Curation 2018 (2018)
Tomonori Hayami, Kota Kasahara, Haruki Nakamura, Junichi Higo
Molecular dynamics coupled with a virtual system for effective conformational sampling. J. Comput. Chem. 39 (19) (2018)
Satoshi Matsuzono, Haruki Nakamura, Daiya Kato, Roshan Lalintha Peiris, Kouta Minamizawa
HaptI/O: Physical Node for the Internet of Haptics. UIST (Adjunct Volume) (2017)
Akira R. Kinjo, Gert-Jan Bekker, Hirofumi Suzuki, Yuko Tsuchiya, Takeshi Kawabata, Yasuyo Ikegawa, Haruki Nakamura
Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures. Nucleic Acids Res. 45 (Database-Issue) (2017)
Kota Kasahara, Neetha Mohan, Ikuo Fukuda, Haruki Nakamura
mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories. Bioinform. 32 (16) (2016)
Gert-Jan Bekker, Haruki Nakamura, Akira R. Kinjo
Molmil: a molecular viewer for the PDB and beyond. J. Cheminformatics 8 (1) (2016)
Noriko Shimba, Narutoshi Kamiya, Haruki Nakamura
Model Building of Antibody-Antigen Complex Structures Using GBSA Scores. J. Chem. Inf. Model. 56 (10) (2016)
Shinji Iida, Tadaaki Mashimo, Takashi Kurosawa, Hironobu Hojo, Hiroya Muta, Yuji Goto, Yoshifumi Fukunishi, Haruki Nakamura, Junichi Higo
Variation of free-energy landscape of the p53 C-terminal domain induced by acetylation: Enhanced conformational sampling. J. Comput. Chem. 37 (31) (2016)
Andrea Schafferhans, Seán I. O'Donoghue, Haruki Nakamura
Web-based Molecular Graphics (NII Shonan Meeting 2016-12). NII Shonan Meet. Rep. 2016 (2016)
Yu Takano, Kazuto Nakata, Yasushige Yonezawa, Haruki Nakamura
Development of massive multilevel molecular dynamics simulation program, platypus (PLATform for dYnamic protein unified simulation), for the elucidation of protein functions. J. Comput. Chem. 37 (12) (2016)
Haruki Nakamura, Nobuhisa Hanamitsu, Junichi Kanebako, Kouta Minamizawa
A Finger Sensor for Sharing Visual and Tactile Experience. AsiaHaptics (2016)
Hirofumi Suzuki, Takeshi Kawabata, Haruki Nakamura
Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB. Bioinform. 32 (4) (2016)
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
Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins. J. Biomed. Semant. 7 (2016)
Junichi Higo, Bhaskar Dasgupta, Tadaaki Mashimo, Kota Kasahara, Yoshifumi Fukunishi, Haruki Nakamura
Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking. J. Comput. Chem. 36 (20) (2015)
Hung Nguyen, Tien Tran, Yoshifumi Fukunishi, Junichi Higo, Haruki Nakamura, Ly Le
Computational Study of Drug Binding Affinity to Influenza A Neuraminidase Using Smooth Reaction Path Generation (SRPG) Method. J. Chem. Inf. Model. 55 (9) (2015)
Haruki Nakamura, Nobuhisa Hanamitsu, Kouta Minamizawa
A(touch)ment: a smartphone extension for instantly sharing visual and tactile experience. AH (2015)
Nobuhisa Hanamitsu, Haruki Nakamura, Masashi Nakatani, Kouta Minamizawa
: a mobile platform to search and share visuo-tactile experiences. SIGGRAPH Asia Emerging Technologies (2015)
Nobuhisa Hanamitsu, Haruki Nakamura, Masashi Nakatani, Kouta Minamizawa
Twech: a mobile platform to search and share visuo-tactile experiences. SIGGRAPH Asia Mobile Graphics and Interactive Applications (2015)
Yoshifumi Fukunishi, Takashi Kurosawa, Yoshiaki Mikami, Haruki Nakamura
Prediction of Synthetic Accessibility Based on Commercially Available Compound Databases. J. Chem. Inf. Model. 54 (12) (2014)
Kazuo Yamashita, Kazuyoshi Ikeda, Karlou Mar Amada, Shide Liang, Yuko Tsuchiya, Haruki Nakamura, Hiroki Shirai, Daron M. Standley
Kotai Antibody Builder: automated high-resolution structural modeling of antibodies. Bioinform. 30 (22) (2014)
Takeshi Kawabata, Haruki Nakamura
3D Flexible Alignment Using 2D Maximum Common Substructure: Dependence of Prediction Accuracy on Target-Reference Chemical Similarity. J. Chem. Inf. Model. 54 (7) (2014)
Helen M. Berman, Gerard J. Kleywegt, Haruki Nakamura, John L. Markley
The Protein Data Bank archive as an open data resource. J. Comput. Aided Mol. Des. 28 (10) (2014)
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
Protein Experimental Information Management System (PREIMS) Based on Ontology: Development and Applications. Inf. Media Technol. 8 (3) (2013)
Akira R. Kinjo, Hirofumi Suzuki, Reiko Yamashita, Yasuyo Ikegawa, Takahiro Kudou, Reiko Igarashi, Yumiko Kengaku, Hasumi Cho, Daron M. Standley, Atsushi Nakagawa, Haruki Nakamura
Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. Nucleic Acids Res. 40 (Database-Issue) (2012)
Ashwini Patil, Kenta Nakai, Haruki Nakamura
HitPredict: a database of quality assessed protein-protein interactions in nine species. Nucleic Acids Res. 39 (Database-Issue) (2011)
Jinzen Ikebe, Koji Umezawa, Narutoshi Kamiya, Takanori Sugihara, Yasushige Yonezawa, Yu Takano, Haruki Nakamura, Junichi Higo
Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water. J. Comput. Chem. 32 (7) (2011)
Mitsuhito Wada, Eiji Kanamori, Haruki Nakamura, Yoshifumi Fukunishi
Selection of In Silico Drug Screening Results for G-Protein-Coupled Receptors by Using Universal Active Probes. J. Chem. Inf. Model. 51 (9) (2011)
Yoshifumi Fukunishi, Haruki Nakamura
Definition of Drug-Likeness for Compound Affinity. J. Chem. Inf. Model. 51 (5) (2011)
Yu Takano, Haruki Nakamura
. J. Comput. Chem. 31 (5) (2010)
Akira R. Kinjo, Reiko Yamashita, Haruki Nakamura
PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan. Database J. Biol. Databases Curation 2010 (2010)
Yoichi Murakami, Ruth V. Spriggs, Haruki Nakamura, Susan Jones
PiRaNhA: a server for the computational prediction of RNA-binding residues in protein sequences. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Daron M. Standley, Reiko Yamashita, Akira R. Kinjo, Hiroyuki Toh, Haruki Nakamura
: balancing sequence and structural information in protein functional mapping. Bioinform. 26 (9) (2010)
Yoshifumi Fukunishi, Kazuki Ohno, Masaya Orita, Haruki Nakamura
Selection of In Silico Drug Screening Results by Using Universal Active Probes (UAPs). J. Chem. Inf. Model. 50 (7) (2010)
Yoshifumi Fukunishi, Tadaaki Mashimo, Masaya Orita, Kazuki Ohno, Haruki Nakamura
In Silico Fragment Screening by Replica Generation (FSRG) Method for Fragment-Based Drug Design. J. Chem. Inf. Model. 49 (4) (2009)
Ruth V. Spriggs, Yoichi Murakami, Haruki Nakamura, Susan Jones
Protein function annotation from sequence: prediction of residues interacting with RNA. Bioinform. 25 (12) (2009)
Séverine Queyroy, Haruki Nakamura, Ikuo Fukuda
Numerical examination of the extended phase-space volume-preserving integrator by the Nosé-Hoover molecular dynamics equations. J. Comput. Chem. 30 (12) (2009)
Yoshifumi Fukunishi, Daisuke Mitomo, Haruki Nakamura
Protein-Ligand Binding Free Energy Calculation by the Smooth Reaction Path Generation (SRPG) Method. J. Chem. Inf. Model. 49 (8) (2009)
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. J. Comput. Chem. 30 (1) (2009)
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
Remediation of the protein data bank archive. Nucleic Acids Res. 36 (Database-Issue) (2008)
Daron M. Standley, Akira R. Kinjo, Kengo Kinoshita, Haruki Nakamura
Protein structure databases with new web services for structural biology and biomedical research. Briefings Bioinform. 9 (4) (2008)
Yoshifumi Fukunishi, Haruki Nakamura
Improvement of Protein-Compound Docking Scores by Using Amino-Acid Sequence Similarities of Proteins. J. Chem. Inf. Model. 48 (1) (2008)
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 Res. 35 (Database-Issue) (2007)
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 Res. 35 (Web-Server-Issue) (2007)
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)
Daron M. Standley, Hiroyuki Toh, Haruki Nakamura
ASH structure alignment package: Sensitivity and selectivity in domain classification. BMC Bioinform. 8 (2007)
Yoshifumi Fukunishi, Shinichi Hojo, Haruki Nakamura
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. 46 (6) (2006)
Yuko Tsuchiya, Kengo Kinoshita, Nobutoshi Ito, Haruki Nakamura
PreBI: prediction of biological interfaces of proteins in crystals. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
Yoshifumi Fukunishi, Satoru Kubota, Haruki Nakamura
Noise Reduction Method for Molecular Interaction Energy: Application to in Silico Drug Screening and in Silico Target Protein Screening. J. Chem. Inf. Model. 46 (5) (2006)
Yoshifumi Fukunishi, Satoru Kubota, Chisato Kanai, Haruki Nakamura
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. 20 (4) (2006)
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
Deploying Scientific Applications to the PRAGMA Grid Testbed: Strategies and Lessons. CCGRID (2006)
John D. Westbrook, Nobutoshi Ito, Haruki Nakamura, Kim Henrick, Helen M. Berman
PDBML: the representation of archival macromolecular structure data in XML. Bioinform. 21 (7) (2005)
Ashwini Patil, Haruki Nakamura
Filtering high-throughput protein-protein interaction data using a combination of genomic features. BMC Bioinform. 6 (2005)
Daron M. Standley, Hiroyuki Toh, Haruki Nakamura
GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures. BMC Bioinform. 6 (2005)
Haruki Nakamura
Protein informatics towards integration of data grid and computing grid. APBC (2005)
Yuko Tsuchiya, Kengo Kinoshita, Haruki Nakamura
PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces. Bioinform. 21 (8) (2005)
Kengo Kinoshita, Haruki Nakamura
eF-site and PDBjViewer: database and viewer for protein functional sites. Bioinform. 20 (8) (2004)
Rie Tatsumi, Yoshifumi Fukunishi, Haruki Nakamura
A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor. J. Comput. Chem. 25 (16) (2004)
Haruki Nakamura, Susumu Date, Hideo Matsuda, Shinji Shimojo
A Challenge towards Next-Generation Research Infrastructure for Advanced Life Science. New Gener. Comput. 22 (2) (2004)
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)
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. J. Comput. Chem. 24 (3) (2003)
Tadasuke Nakagawa, Takanori Tanaka, Takenao Ohkawa, Haruki Nakamura
A filtering method for high-speed retrieval of similar active sites. Inf. Sci. 146 (1-4) (2002)
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)
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. J. Comput. Chem. 23 (4) (2002)
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) (2002)
Tadasuke Nakagawa, Takanori Tanaka, Takenao Ohkawa, Haruki Nakamura
A Filtering Method for High-Speed Retrieval of Similar Active Sites. JCIS (2002)
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. J. Comput. Chem. 22 (16) (2001)
Satoshi Ono, Nobuyuki Nakajima, Junichi Higo, Haruki Nakamura
Peptide free-energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95. J. Comput. Chem. 21 (9) (2000)
Kenji Morikami, Takahisa Nakai, Akinori Kidera, Minoru Saito, Haruki Nakamura
Presto(protein Engineering Simulator): A Vectorized Molecular Mechanics Program for Biopolymers. Comput. Chem. 16 (3) (1992)