Haruki Nakamura

According to our database1, Haruki Nakamura authored at least 68 papers between 1992 and 2019.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.



In proceedings 
PhD thesis 


On csauthors.net:


Hydrogen bond donors and acceptors are generally depolarized in α-helices as revealed by a molecular tailoring approach.
Journal of Computational Chemistry, 2019

Density functional study of porphyrin distortion effects on redox potential of heme.
Journal of Computational Chemistry, 2018

Molecular dynamics coupled with a virtual system for effective conformational sampling.
Journal of Computational Chemistry, 2018

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.
Database, 2018

Construction of Haptic Experience Sharing Platform.
Proceedings of the 2018 ACM International Joint Conference and 2018 International Symposium on Pervasive and Ubiquitous Computing and Wearable Computers, 2018

HaptI/O: Physical I/O Node over the Internet.
Proceedings of the Haptics: Science, Technology, and Applications, 2018

Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures.
Nucleic Acids Research, 2017

HaptI/O: Physical Node for the Internet of Haptics.
Proceedings of the Adjunct Publication of the 30th Annual ACM Symposium on User Interface Software and Technology, 2017

Web-based Molecular Graphics (NII Shonan Meeting 2016-12).
NII Shonan Meet. Rep., 2016

Model Building of Antibody-Antigen Complex Structures Using GBSA Scores.
Journal of Chemical Information and Modeling, 2016

Molmil: a molecular viewer for the PDB and beyond.
J. Cheminformatics, 2016

Development of massive multilevel molecular dynamics simulation program, platypus (PLATform for dYnamic protein unified simulation), for the elucidation of protein functions.
Journal of Computational Chemistry, 2016

Variation of free-energy landscape of the p53 C-terminal domain induced by acetylation: Enhanced conformational sampling.
Journal of Computational Chemistry, 2016

Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins.
J. Biomedical Semantics, 2016

Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB.
Bioinformatics, 2016

mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories.
Bioinformatics, 2016

A Finger Sensor for Sharing Visual and Tactile Experience.
Proceedings of the Haptic Interaction, 2016

Computational Study of Drug Binding Affinity to Influenza A Neuraminidase Using Smooth Reaction Path Generation (SRPG) Method.
Journal of Chemical Information and Modeling, 2015

Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking.
Journal of Computational Chemistry, 2015

Twech: a mobile platform to search and share visuo-tactile experiences.
Proceedings of the SIGGRAPH Asia 2015 Emerging Technologies, 2015

Twech: a mobile platform to search and share visuo-tactile experiences.
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

3D Flexible Alignment Using 2D Maximum Common Substructure: Dependence of Prediction Accuracy on Target-Reference Chemical Similarity.
Journal of Chemical Information and Modeling, 2014

Prediction of Synthetic Accessibility Based on Commercially Available Compound Databases.
Journal of Chemical Information and Modeling, 2014

The Protein Data Bank archive as an open data resource.
Journal of Computer-Aided Molecular Design, 2014

Kotai Antibody Builder: automated high-resolution structural modeling of antibodies.
Bioinformatics, 2014

Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format.
Nucleic Acids Research, 2012

HitPredict: a database of quality assessed protein-protein interactions in nine species.
Nucleic Acids Research, 2011

Selection of In Silico Drug Screening Results for G-Protein-Coupled Receptors by Using Universal Active Probes.
Journal of Chemical Information and Modeling, 2011

Definition of Drug-Likeness for Compound Affinity.
Journal of Chemical Information and Modeling, 2011

Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water.
Journal of Computational Chemistry, 2011

PiRaNhA: a server for the computational prediction of RNA-binding residues in protein sequences.
Nucleic Acids Research, 2010

Selection of In Silico Drug Screening Results by Using Universal Active Probes (UAPs).
Journal of Chemical Information and Modeling, 2010

Electronic structures of heme a of cytochrome c oxidase in the redox states - Charge density migration to the propionate groups of heme a.
Journal of Computational Chemistry, 2010

SeSAW: balancing sequence and structural information in protein functional mapping.
Bioinformatics, 2010

PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan.
Database, 2010

In Silico Fragment Screening by Replica Generation (FSRG) Method for Fragment-Based Drug Design.
Journal of Chemical Information and Modeling, 2009

Protein-Ligand Binding Free Energy Calculation by the Smooth Reaction Path Generation (SRPG) Method.
Journal of Chemical Information and Modeling, 2009

Numerical examination of the extended phase-space volume-preserving integrator by the Nosé-Hoover molecular dynamics equations.
Journal of Computational Chemistry, 2009

Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems.
Journal of Computational Chemistry, 2009

Protein function annotation from sequence: prediction of residues interacting with RNA.
Bioinformatics, 2009

Remediation of the protein data bank archive.
Nucleic Acids Research, 2008

Improvement of Protein-Compound Docking Scores by Using Amino-Acid Sequence Similarities of Proteins.
Journal of Chemical Information and Modeling, 2008

Protein structure databases with new web services for structural biology and biomedical research.
Briefings in Bioinformatics, 2008

eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape.
Nucleic Acids Research, 2007

The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data.
Nucleic Acids Research, 2007

ASH structure alignment package: Sensitivity and selectivity in domain classification.
BMC Bioinformatics, 2007

A Grid-Ready Clinical Database for Parkinson's Disease Research and Diagnosis.
Proceedings of the 20th IEEE International Symposium on Computer-Based Medical Systems (CBMS 2007), 2007

PreBI: prediction of biological interfaces of proteins in crystals.
Nucleic Acids Research, 2006

Noise Reduction Method for Molecular Interaction Energy: Application to in Silico Drug Screening and in Silico Target Protein Screening.
Journal of Chemical Information and Modeling, 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.
Journal of Chemical Information and Modeling, 2006

A Virtual Active Compound Produced from the Negative Image of a Ligand-binding Pocket, and its Application to in-silico Drug Screening.
Journal of Computer-Aided Molecular Design, 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

GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures.
BMC Bioinformatics, 2005

Filtering high-throughput protein-protein interaction data using a combination of genomic features.
BMC Bioinformatics, 2005

PDBML: the representation of archival macromolecular structure data in XML.
Bioinformatics, 2005

PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces.
Bioinformatics, 2005

Protein informatics towards integration of data grid and computing grid.
Proceedings of 3rd Asia-Pacific Bioinformatics Conference, 17-21 January 2005, Singapore, 2005

A Challenge towards Next-Generation Research Infrastructure for Advanced Life Science.
New Generation Comput., 2004

eF-site and PDBjViewer: database and viewer for protein functional sites.
Bioinformatics, 2004

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, 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

Calibration of force-field dependency in free energy landscapes of peptide conformations by quantum chemical calculations.
Journal of Computational Chemistry, 2002

A Filtering Method for High-Speed Retrieval of Similar Active Sites.
Proceedings of the 6th Joint Conference on Information Science, 2002

A Method of Comparing Protein Molecular Surface Based on Normal Vectors with Attributes and Its Application to Function Identification.
Proceedings of the 6th Joint Conference on Information Science, 2002

Collective motions of myosin head derived from backbone molecular dynamics and combination with X-ray solution scattering data.
Journal of Computational Chemistry, 2001

Peptide free-energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95.
Journal of Computational Chemistry, 2000

Presto(protein Engineering Simulator): A Vectorized Molecular Mechanics Program for Biopolymers.
Computers & Chemistry, 1992