Haruki Nakamura
Orcid: 0000-0001-6690-5863
According to our database1,
Haruki Nakamura
authored at least 71 papers
between 1992 and 2020.
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Bibliography
2020
Molecular Interaction Mechanism of a 14-3-3 Protein with a Phosphorylated Peptide Elucidated by Enhanced Conformational Sampling.
J. Chem. Inf. Model., 2020
2019
Hydrogen bond donors and acceptors are generally depolarized in α-helices as revealed by a molecular tailoring approach.
J. Comput. Chem., 2019
Multidimensional virtual-system coupled canonical molecular dynamics to compute free-energy landscapes of peptide multimer assembly.
J. Comput. Chem., 2019
2018
J. Comput. Chem., 2018
Molecular dynamics coupled with a virtual system for effective conformational sampling.
J. Comput. Chem., 2018
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.
Database J. Biol. Databases Curation, 2018
Proceedings of the 2018 ACM International Joint Conference and 2018 International Symposium on Pervasive and Ubiquitous Computing and Wearable Computers, 2018
Proceedings of the Haptics: Science, Technology, and Applications, 2018
2017
Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures.
Nucleic Acids Res., 2017
Proceedings of the Adjunct Publication of the 30th Annual ACM Symposium on User Interface Software and Technology, 2017
2016
NII Shonan Meet. Rep., 2016
J. Chem. Inf. Model., 2016
Development of massive multilevel molecular dynamics simulation program, platypus (PLATform for dYnamic protein unified simulation), for the elucidation of protein functions.
J. Comput. Chem., 2016
Variation of free-energy landscape of the p53 C-terminal domain induced by acetylation: Enhanced conformational sampling.
J. Comput. Chem., 2016
Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins.
J. Biomed. Semant., 2016
Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB.
Bioinform., 2016
mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories.
Bioinform., 2016
Proceedings of the Haptic Interaction, 2016
2015
Computational Study of Drug Binding Affinity to Influenza A Neuraminidase Using Smooth Reaction Path Generation (SRPG) Method.
J. Chem. Inf. Model., 2015
Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking.
J. Comput. Chem., 2015
Proceedings of the SIGGRAPH Asia 2015 Emerging Technologies, 2015
Proceedings of the SIGGRAPH Asia 2015 Mobile Graphics and Interactive Applications, 2015
A(touch)ment: a smartphone extension for instantly sharing visual and tactile experience.
Proceedings of the 6th Augmented Human International Conference, 2015
2014
3D Flexible Alignment Using 2D Maximum Common Substructure: Dependence of Prediction Accuracy on Target-Reference Chemical Similarity.
J. Chem. Inf. Model., 2014
Prediction of Synthetic Accessibility Based on Commercially Available Compound Databases.
J. Chem. Inf. Model., 2014
J. Comput. Aided Mol. Des., 2014
Bioinform., 2014
2012
Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format.
Nucleic Acids Res., 2012
2011
HitPredict: a database of quality assessed protein-protein interactions in nine species.
Nucleic Acids Res., 2011
Selection of In Silico Drug Screening Results for G-Protein-Coupled Receptors by Using Universal Active Probes.
J. Chem. Inf. Model., 2011
Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water.
J. Comput. Chem., 2011
2010
PiRaNhA: a server for the computational prediction of RNA-binding residues in protein sequences.
Nucleic Acids Res., 2010
Selection of In Silico Drug Screening Results by Using Universal Active Probes (UAPs).
J. Chem. Inf. Model., 2010
Electronic structures of heme <i>a</i> of cytochrome <i>c</i> oxidase in the redox states - Charge density migration to the propionate groups of heme <i>a</i>.
J. Comput. Chem., 2010
<i>SeSAW</i>: balancing sequence and structural information in protein functional mapping.
Bioinform., 2010
PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan.
Database J. Biol. Databases Curation, 2010
2009
In Silico Fragment Screening by Replica Generation (FSRG) Method for Fragment-Based Drug Design.
J. Chem. Inf. Model., 2009
Protein-Ligand Binding Free Energy Calculation by the Smooth Reaction Path Generation (SRPG) Method.
J. Chem. Inf. Model., 2009
Numerical examination of the extended phase-space volume-preserving integrator by the Nosé-Hoover molecular dynamics equations.
J. Comput. Chem., 2009
Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems.
J. Comput. Chem., 2009
Protein function annotation from sequence: prediction of residues interacting with RNA.
Bioinform., 2009
2008
Improvement of Protein-Compound Docking Scores by Using Amino-Acid Sequence Similarities of Proteins.
J. Chem. Inf. Model., 2008
Protein structure databases with new web services for structural biology and biomedical research.
Briefings Bioinform., 2008
2007
eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape.
Nucleic Acids Res., 2007
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data.
Nucleic Acids Res., 2007
ASH structure alignment package: Sensitivity and selectivity in domain classification.
BMC Bioinform., 2007
Proceedings of the 20th IEEE International Symposium on Computer-Based Medical Systems (CBMS 2007), 2007
2006
Nucleic Acids Res., 2006
Noise Reduction Method for Molecular Interaction Energy: Application to in Silico Drug Screening and in Silico Target Protein Screening.
J. Chem. Inf. Model., 2006
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., 2006
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., 2006
Deploying Scientific Applications to the PRAGMA Grid Testbed: Strategies and Lessons.
Proceedings of the Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2006), 2006
2005
GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures.
BMC Bioinform., 2005
Filtering high-throughput protein-protein interaction data using a combination of genomic features.
BMC Bioinform., 2005
Bioinform., 2005
Bioinform., 2005
Proceedings of 3rd Asia-Pacific Bioinformatics Conference, 17-21 January 2005, Singapore, 2005
2004
A Challenge towards Next-Generation Research Infrastructure for Advanced Life Science.
New Gener. Comput., 2004
A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor.
J. Comput. Chem., 2004
Bioinform., 2004
2003
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., 2003
Information Extraction from Semi-Structured Data in the Protein Data Bank by Induction of a Data Description Pattern.
Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Scienes, 2003
2002
Calibration of force-field dependency in free energy landscapes of peptide conformations by quantum chemical calculations.
J. Comput. Chem., 2002
A method of comparing protein molecular surface based on normal vectors with attributes and its application to function identification.
Inf. Sci., 2002
2001
Collective motions of myosin head derived from backbone molecular dynamics and combination with X-ray solution scattering data.
J. Comput. Chem., 2001
2000
Peptide free-energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95.
J. Comput. Chem., 2000
1992
Presto(protein Engineering Simulator): A Vectorized Molecular Mechanics Program for Biopolymers.
Comput. Chem., 1992