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Haruki Nakamura
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2020 – today
- 2020
- [j61]Junichi Higo
, Takeshi Kawabata
Molecular Interaction Mechanism of a 14-3-3 Protein with a Phosphorylated Peptide Elucidated by Enhanced Conformational Sampling. J. Chem. Inf. Model. 60(10): 4867-4880 (2020)
2010 – 2019
- 2019
- [j60]Hiroko X. Kondo
Hydrogen bond donors and acceptors are generally depolarized in α-helices as revealed by a molecular tailoring approach. J. Comput. Chem. 40(23): 2043-2052 (2019) - [j59]Tomonori Hayami, Junichi Higo
Multidimensional virtual-system coupled canonical molecular dynamics to compute free-energy landscapes of peptide multimer assembly. J. Comput. Chem. 40(28): 2453-2463 (2019) - 2018
- [j58]Jasmine Young
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. Database J. Biol. Databases Curation 2018: bay002 (2018) - [j57]Yasuhiro Imada, Haruki Nakamura, Yu Takano
Density functional study of porphyrin distortion effects on redox potential of heme. J. Comput. Chem. 39(3): 143-150 (2018) - [j56]Tomonori Hayami, Kota Kasahara
Molecular dynamics coupled with a virtual system for effective conformational sampling. J. Comput. Chem. 39(19): 1291-1299 (2018) - [c13]Satoshi Matsuzono, Haruki Nakamura, Daiya Kato, Roshan Lalintha Peiris
HaptI/O: Physical I/O Node over the Internet. EuroHaptics (2) 2018: 193-203 - [c12]Haruki Nakamura, Daiya Kato, Roshan Lalintha Peiris
Construction of Haptic Experience Sharing Platform. UbiComp/ISWC Adjunct 2018: 174-177 - 2017
- [j55]Akira R. Kinjo
Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures. Nucleic Acids Res. 45(Database-Issue): D282-D288 (2017) - [c11]Satoshi Matsuzono, Haruki Nakamura, Daiya Kato, Roshan Lalintha Peiris
HaptI/O: Physical Node for the Internet of Haptics. UIST (Adjunct Volume) 2017: 53-55 - 2016
- [j54]Hirofumi Suzuki, Takeshi Kawabata
Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB. Bioinform. 32(4): 619-620 (2016) - [j53]Kota Kasahara
mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories. Bioinform. 32(16): 2531-2533 (2016) - [j52]Masashi Yokochi, Naohiro Kobayashi, Eldon L. Ulrich, Akira R. Kinjo
Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins. J. Biomed. Semant. 7: 16 (2016) - [j51]Yu Takano
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): 1125-1132 (2016) - [j50]Shinji Iida, Tadaaki Mashimo, Takashi Kurosawa, Hironobu Hojo, Hiroya Muta, Yuji Goto, Yoshifumi Fukunishi
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) - [j49]Gert-Jan Bekker
Molmil: a molecular viewer for the PDB and beyond. J. Cheminformatics 8(1): 42:1-42:5 (2016) - [j48]Noriko Shimba, Narutoshi Kamiya, Haruki Nakamura:
Model Building of Antibody-Antigen Complex Structures Using GBSA Scores. J. Chem. Inf. Model. 56(10): 2005-2012 (2016) - [c10]Haruki Nakamura, Nobuhisa Hanamitsu, Junichi Kanebako, Kouta Minamizawa:
A Finger Sensor for Sharing Visual and Tactile Experience. AsiaHaptics 2016: 305-307 - [i1]Andrea Schafferhans, Seán I. O'Donoghue, Haruki Nakamura:
Web-based Molecular Graphics (NII Shonan Meeting 2016-12). NII Shonan Meet. Rep. 2016 (2016) - 2015
- [j47]Junichi Higo, Bhaskar Dasgupta
Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking. J. Comput. Chem. 36(20): 1489-1501 (2015) - [j46]Hung Nguyen
Computational Study of Drug Binding Affinity to Influenza A Neuraminidase Using Smooth Reaction Path Generation (SRPG) Method. J. Chem. Inf. Model. 55(9): 1936-1943 (2015) - [c9]Haruki Nakamura, Nobuhisa Hanamitsu, Kouta Minamizawa:
A(touch)ment: a smartphone extension for instantly sharing visual and tactile experience. AH 2015: 223-224 - [c8]Nobuhisa Hanamitsu, Haruki Nakamura, Masashi Nakatani
Twech: a mobile platform to search and share visuo-tactile experiences. SIGGRAPH Asia Mobile Graphics and Interactive Applications 2015: 10:1-10:3 - [c7]Nobuhisa Hanamitsu, Haruki Nakamura, Masashi Nakatani
Twech: a mobile platform to search and share visuo-tactile experiences. SIGGRAPH Asia Emerging Technologies 2015: 26:1-26:2 - 2014
- [j45]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): 3279-3280 (2014) - [j44]Helen M. Berman
The Protein Data Bank archive as an open data resource. J. Comput. Aided Mol. Des. 28(10): 1009-1014 (2014) - [j43]Takeshi Kawabata
3D Flexible Alignment Using 2D Maximum Common Substructure: Dependence of Prediction Accuracy on Target-Reference Chemical Similarity. J. Chem. Inf. Model. 54(7): 1850-1863 (2014) - [j42]Yoshifumi Fukunishi
Prediction of Synthetic Accessibility Based on Commercially Available Compound Databases. J. Chem. Inf. Model. 54(12): 3259-3267 (2014) - 2013
- [j41]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): 875-883 (2013) - 2012
- [j40]Akira R. Kinjo
Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. Nucleic Acids Res. 40(Database-Issue): 453-460 (2012) - 2011
- [j39]Jinzen Ikebe
Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water. J. Comput. Chem. 32(7): 1286-1297 (2011) - [j38]Yoshifumi Fukunishi
Definition of Drug-Likeness for Compound Affinity. J. Chem. Inf. Model. 51(5): 1012-1016 (2011) - [j37]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): 2398-2407 (2011) - [j36]Ashwini Patil
HitPredict: a database of quality assessed protein-protein interactions in nine species. Nucleic Acids Res. 39(Database-Issue): 744-749 (2011) - 2010
- [j35]Akira R. Kinjo
PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan. Database J. Biol. Databases Curation 2010 (2010) - [j34]Daron M. Standley, Reiko Yamashita, Akira R. Kinjo
SeSAW: balancing sequence and structural information in protein functional mapping. Bioinform. 26(9): 1258-1259 (2010) - [j33]Yu Takano
Electronic structures of heme a of cytochrome c oxidase in the redox states - Charge density migration to the propionate groups of heme a. J. Comput. Chem. 31(5): 954-962 (2010) - [j32]Yoshifumi Fukunishi
Selection of In Silico Drug Screening Results by Using Universal Active Probes (UAPs). J. Chem. Inf. Model. 50(7): 1233-1240 (2010) - [j31]Yoichi Murakami, Ruth V. Spriggs
PiRaNhA: a server for the computational prediction of RNA-binding residues in protein sequences. Nucleic Acids Res. 38(Web-Server-Issue): 412-416 (2010)
2000 – 2009
- 2009
- [j30]Ruth V. Spriggs
Protein function annotation from sequence: prediction of residues interacting with RNA. Bioinform. 25(12): 1492-1497 (2009) - [j29]Susumu Date, Kazunori Nozaki, Haruki Nakamura, Saburo Sakoda, Shinji Shimojo:
A Grid-aware Access Control Mechanism in a Clinical Database for Parkinson's Disease Research and Diagnosis. Inf. Media Technol. 4(2): 583-593 (2009) - [j28]Gota Kikugawa, Rossen Apostolov, Narutoshi Kamiya, Makoto Taiji
Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems. J. Comput. Chem. 30(1): 110-118 (2009) - [j27]Séverine Queyroy
Numerical examination of the extended phase-space volume-preserving integrator by the Nosé-Hoover molecular dynamics equations. J. Comput. Chem. 30(12): 1799-1815 (2009) - [j26]Yoshifumi Fukunishi
In Silico Fragment Screening by Replica Generation (FSRG) Method for Fragment-Based Drug Design. J. Chem. Inf. Model. 49(4): 925-933 (2009) - [j25]Yoshifumi Fukunishi
Protein-Ligand Binding Free Energy Calculation by the Smooth Reaction Path Generation (SRPG) Method. J. Chem. Inf. Model. 49(8): 1944-1951 (2009) - 2008
- [j24]Daron M. Standley, Akira R. Kinjo
Protein structure databases with new web services for structural biology and biomedical research. Briefings Bioinform. 9(4): 276-285 (2008) - [j23]Yoshifumi Fukunishi
Improvement of Protein-Compound Docking Scores by Using Amino-Acid Sequence Similarities of Proteins. J. Chem. Inf. Model. 48(1): 148-156 (2008) - [j22]Kim Henrick, Zukang Feng, Wolfgang Bluhm, Dimitris Dimitropoulos, Jurgen F. Doreleijers, Shuchismita Dutta
Remediation of the protein data bank archive. Nucleic Acids Res. 36(Database-Issue): 426-433 (2008) - 2007
- [j21]Daron M. Standley, Hiroyuki Toh, Haruki Nakamura:
ASH structure alignment package: Sensitivity and selectivity in domain classification. BMC Bioinform. 8 (2007) - [j20]Helen M. Berman
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res. 35(Database-Issue): 301-303 (2007) - [j19]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): 398-402 (2007) - [c6]Susumu Date
A Grid-Ready Clinical Database for Parkinson's Disease Research and Diagnosis. CBMS 2007: 483-488 - 2006
- [j18]Yoshifumi Fukunishi
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): 237-248 (2006) - [j17]Yoshifumi Fukunishi
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): 2071-2084 (2006) - [j16]Yoshifumi Fukunishi
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): 2610-2622 (2006) - [j15]Yuko Tsuchiya, Kengo Kinoshita, Nobutoshi Ito, Haruki Nakamura:
PreBI: prediction of biological interfaces of proteins in crystals. Nucleic Acids Res. 34(Web-Server-Issue): 20-24 (2006) - [c5]David Abramson
Deploying Scientific Applications to the PRAGMA Grid Testbed: Strategies and Lessons. CCGRID 2006: 241-248 - 2005
- [j14]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): 988-992 (2005) - [j13]Yuko Tsuchiya, Kengo Kinoshita, Haruki Nakamura:
PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces. Bioinform. 21(8): 1721-1723 (2005) - [j12]Ashwini Patil
Filtering high-throughput protein-protein interaction data using a combination of genomic features. BMC Bioinform. 6: 100 (2005) - [j11]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: 221 (2005) - [c4]Haruki Nakamura:
Protein informatics towards integration of data grid and computing grid. APBC 2005: 359-362 - 2004
- [j10]Kengo Kinoshita, Haruki Nakamura:
eF-site and PDBjViewer: database and viewer for protein functional sites. Bioinform. 20(8): 1329-1330 (2004) - [j9]Rie Tatsumi
A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor. J. Comput. Chem. 25(16): 1995-2005 (2004) - [j8]Haruki Nakamura, Susumu Date
A Challenge towards Next-Generation Research Infrastructure for Advanced Life Science. New Gener. Comput. 22(2): 157-166 (2004) - 2003
- [j7]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): 310-318 (2003) - [c3]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 - 2002
- [j6]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) - [j5]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) - [j4]Satoshi Ono
Calibration of force-field dependency in free energy landscapes of peptide conformations by quantum chemical calculations. J. Comput. Chem. 23(4): 470-476 (2002) - [c2]Tadasuke Nakagawa, Takanori Tanaka, Takenao Ohkawa, Haruki Nakamura:
A Filtering Method for High-Speed Retrieval of Similar Active Sites. JCIS 2002: 1207-1212 - [c1]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 - 2001
- [j3]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): 1983-1994 (2001) - 2000
- [j2]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): 748-762 (2000)
1990 – 1999
- 1992
- [j1]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): 243-248 (1992)
Coauthor Index
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