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List of works by Haruki Nakamura

A critical appraisal of the zero-multipole method: Structural, thermodynamic, dielectric, and dynamical properties of a water system.

scientific article published in March 2016

A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor

scientific article published in December 2004

A method to enhance the hit ratio by a combination of structure-based drug screening and ligand-based screening.

scientific article

A new method for in-silico drug screening and similarity search using molecular dynamics maximum volume overlap (MD-MVO) method

scientific article

A novel approach of dynamic cross correlation analysis on molecular dynamics simulations and its application to Ets1 dimer-DNA complex

scientific article (publication date: 2014)

A virtual-system coupled multicanonical molecular dynamics simulation: Principles and applications to free-energy landscape of protein–protein interaction with an all-atom model in explicit solvent ⬇️

scientific article published on May 14, 2013

ASH structure alignment package: sensitivity and selectivity in domain classification

scientific article

Ab initio simulation of a 57-residue protein in explicit solvent reproduces the native conformation in the lowest free-energy cluster

scientific article

Accurate Prediction of Complex Structure and Affinity for a Flexible Protein Receptor and Its Inhibitor

scientific article published on 8 May 2017

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

scientific article

Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity

scientific article published on 12 July 2006

Announcing the worldwide Protein Data Bank

scientific article (publication date: December 2003)

Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems

scientific article published in January 2009

Big data science at AMED-BINDS

scientific article published on 06 February 2020

BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions

scientific article

Blind prediction of interfacial water positions in CAPRI

scientific article

CAD-ICAD complex structure derived from saturation transfer experiment and simulated annealing without using pairwise NOE information

scientific article

Classification of heterodimer interfaces using docking models and construction of scoring functions for the complex structure prediction

scientific article

Comment on on the propagation of errors by Jaskolski (2013).

scientific article published on 19 November 2013

Comment on timely deposition of macromolecular structures is necessary for peer review by Joosten et al. (2013).

scientific article published on 19 November 2013

Community-wide assessment of protein-interface modeling suggests improvements to design methodology

scientific article

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

scientific article

Composite Structural Motifs of Binding Sites for Delineating Biological Functions of Proteins ⬇️

scientific article published on February 8, 2012

Comprehensive structural classification of ligand-binding motifs in proteins

scientific article published on February 2009

Computer-aided antibody design

scientific article

Conformational Ensembles of an Intrinsically Disordered Protein pKID with and without a KIX Domain in Explicit Solvent Investigated by All-Atom Multicanonical Molecular Dynamics

scientific article published on 22 February 2012

Conformational requirement on peptides to exert laminin's activities and search for protein segments with laminin's activities

scientific article published on January 2009

Conformational transition states of a beta-hairpin peptide between the ordered and disordered conformations in explicit water

scientific article

Correction: Patil, A. et al. Hub Promiscuity in Protein-Protein Interaction Networks. Int. J. Mol. Sci. 2010, 11, 1930-1943. ⬇️

scientific article published on 27 July 2010

Counterbalance of ligand‐ and self‐coupled motions characterizes multispecificity of ubiquitin ⬇️

scientific article published on December 17, 2012

Creation of a type 1 blue copper site within a de novo coiled-coil protein scaffold

scientific article published on 2 December 2010

Crystal structure of the conserved protein TT1542 fromThermus thermophilusHB8

scientific article

Data Deposition and Annotation at the Worldwide Protein Data Bank

article by Shuchismita Dutta et al published 10 December 2008 in Molecular Biotechnology

Data deposition and annotation at the worldwide protein data bank

scientific article

Definition of Drug-Likeness for Compound Affinity ⬇️

scientific article published on April 27, 2011

Density functional study of porphyrin distortion effects on redox potential of heme

scientific article published on 2 September 2017

Detecting local structural similarity in proteins by maximizing number of equivalent residues

scientific article published in November 2004

Determination of multicanonical weight based on a stochastic model of sampling dynamics

scientific article published on 26 August 2003

Development of massive multilevel molecular dynamics simulation program, Platypus (PLATform for dYnamic Protein Unified Simulation), for the elucidation of protein functions

scientific article published on 4 March 2016

Discrimination between biological interfaces and crystal-packing contacts

scientific article

Docking of protein molecular surfaces with evolutionary trace analysis

scientific article published in December 2007

Domain distribution and intrinsic disorder in hubs in the human protein-protein interaction network

scientific article published on August 2010

Drug Development Value Chain Constructed by Collaboration Between The SOSHO Project and The NPO BIOGRID

article

Dynamical origin of enhanced conformational searches of Tsallis statistics sampling

scientific article

Dynamical origin of uniform sampling in multicanonical ensemble

scientific article published on 29 January 2003

Elastic properties of dynein motor domain obtained from all-atom molecular dynamics simulations

scientific article published on 21 June 2016

Electronic structures of heme a of cytochrome c oxidase in the redox states--charge density migration to the propionate groups of heme a.

scientific article published in April 2010

Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes ⬇️

scientific article published on January 11, 2012

Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation

scientific article

Enhancement of canonical sampling by virtual-state transitions.

scientific article

Exhaustive comparison and classification of ligand‐binding surfaces in proteins ⬇️

scientific article published on 04 September 2013

Extraction of recombinant protein from Escherichia coli by using a novel cell autolysis activity of VanX ⬇️

scientific article published on April 25, 2013

Flexible docking of an amyloid-forming peptide from beta(2)-microglobulin

scientific article published in 2006

Free Energy Landscapes of Alanine Dipeptide in Explicit Water Reproduced by the Force-Switching Wolf Method

scientific article published on 30 March 2011

Functional Structural Motifs for Protein–Ligand, Protein–Protein, and Protein–Nucleic Acid Interactions and their Connection to Supersecondary Structures ⬇️

scientific article published on January 1, 2013

GASH: an improved algorithm for maximizing the number of equivalent residues between two protein structures

scientific article

HINT: a database of annotated protein-protein interactions and their homologs

scientific article published on 28 February 2005

High-resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations

scientific article published on 13 May 2014

HitPredict: a database of quality assessed protein–protein interactions in nine species ⬇️

scientific article published on October 14, 2010

How community has shaped the Protein Data Bank

scientific article

Hub promiscuity in protein-protein interaction networks

scientific article published on 26 April 2010

Hydrogen bond donors and acceptors are generally depolarized in α-helices as revealed by a molecular tailoring approach

scientific article published on 17 May 2019

Identification of protein biochemical functions by similarity search using the molecular surface database eF-site

scientific article published in August 2003

Identification of the ligand binding sites on the molecular surface of proteins

scientific article published on 2 February 2005

Improved estimation of protein-ligand binding free energy by using the ligand-entropy and mobility of water molecules

scientific article published on 26 April 2013

Improvement of protein-compound docking scores by using amino-acid sequence similarities of proteins.

scientific article

In silico fragment screening by replica generation (FSRG) method for fragment-based drug design

scientific article

In silico prediction of the chemical block of human ether-a-go-go-related gene (hERG) K+ current

scientific article published on 27 November 2008

Integration of ligand-based drug screening with structure-based drug screening by combining maximum volume overlapping score with ligand docking

scientific article published on 04 December 2012

Intra- and intermolecular interaction inducing pyramidalization on both sides of a proline dipeptide during isomerization: an ab initio QM/MM molecular dynamics simulation study in explicit water

scientific article published in April 2009

Intramolecular interaction of SUR2 subtypes for intracellular ADP-Induced differential control of K(ATP) channels

scientific article published in March 2002

Kotai Antibody Builder: automated high-resolution structural modeling of antibodies

scientific article

Membrane attachment facilitates ligand access to the active site in monoamine oxidase A.

scientific article

Model building of a protein-protein complexed structure using saturation transfer and residual dipolar coupling without paired intermolecular NOE.

scientific article published in July 2004

Molecular dynamics scheme for precise estimation of electrostatic interaction via zero-dipole summation principle ⬇️

scientific article published on April 28, 2011

Molecular dynamics simulations of double-stranded DNA in an explicit solvent model with the zero-dipole summation method

scientific article

Molecular mechanisms of cooperative binding of transcription factors Runx1-CBFβ-Ets1 on the TCRα gene enhancer

scientific article

Molecular modeling of vasopressin receptor andin silicoscreening of V1b receptor antagonists ⬇️

scientific article published on May 17, 2013

Molmil: a molecular viewer for the PDB and beyond

scientific article

Multi-dimensional virtual system introduced to enhance canonical sampling

scientific article published in October 2017

Multicanonical molecular dynamics algorithm employing an adaptive force-biased iteration scheme

scientific article published on 17 November 2004

Mutational analysis of block and facilitation of HERG current by a class III anti-arrhythmic agent, nifekalant

scientific article published in May 2007

Mutational and structural analyses of Caldanaerobius polysaccharolyticus Man5B reveal novel active site residues for family 5 glycoside hydrolases

scientific article

Nature of protein family signatures: insights from singular value analysis of position-specific scoring matrices

scientific article

New progress in crystallization technology of membrane protein and introduction of pharamaceutical innovation value chain

scientific article

Noise reduction method for molecular interaction energy: application to in silico drug screening and in silico target protein screening.

scientific article

Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB

scientific article published on 27 October 2015

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive

scientific article (publication date: March 2017)

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

scientific article published on 18 June 2015

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop

scientific article

PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models

scientific article

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

scientific article

PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan

scientific article

Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi-modal interaction ensemble to an auto-inhibitory state

scientific article published on 4 January 2018

PiRaNhA: a server for the computational prediction of RNA-binding residues in protein sequences

scientific article published on 27 May 2010

PreBI: prediction of biological interfaces of proteins in crystals

scientific article published on July 2006

Prediction of Protein-compound Binding Energies from Known Activity Data: Docking-score-based Method and its Applications

scientific article published on 14 February 2018

Prediction of ligand‐binding sites of proteins by molecular docking calculation for a random ligand library ⬇️

scientific article published on January 1, 2011

Prediction of synthetic accessibility based on commercially available compound databases

scientific article

Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive

scientific article

Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka University ⬇️

scientific article published on July 28, 2011

Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format

scientific article

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

scientific article

Protein informatics towards function identification

scientific article

Protein-inhibitor flexible docking by a multicanonical sampling: native complex structure with the lowest free energy and a free-energy barrier distinguishing the native complex from the others

scientific article published in January 2008

Protein-ligand binding free energy calculation by the Smooth Reaction Path Generation (SRPG) Method

scientific article published in August 2009

Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins

scientific article

Realism about PDB.

scientific article

Remediation of the protein data bank archive

scientific article

Response to On prompt update of literature references in the Protein Data Bank

scientific article published on 30 September 2014

Revisiting antibody modeling assessment for CDR-H3 loop

scientific article published on 11 August 2016

Rigid‐body motions of interacting proteins dominate multispecific binding of ubiquitin in a shape‐dependent manner ⬇️

scientific article published on August 31, 2013

Safeguarding the integrity of protein archive

scientific article published on January 2010

SeSAW: balancing sequence and structural information in protein functional mapping

scientific article published on 17 March 2010

Selection of in silico drug screening results by using universal active probes (UAPs).

scientific article

Similarity search for local protein structures at atomic resolution by exploiting a database management system

scientific article published on 28 December 2007

Simple and accurate scheme to compute electrostatic interaction: zero-dipole summation technique for molecular system and application to bulk water

scientific article published in August 2012

Simple and effective application of the Wang-Landau method for multicanonical molecular dynamics simulation

scientific article published in January 2011

Specific non-local interactions are not necessary for recovering native protein dynamics

scientific article

Statistical estimation of the protein-ligand binding free energy based on direct protein-ligand interaction obtained by molecular dynamics simulation

scientific article published on 28 September 2012

Structural classification of CDR-H3 revisited: a lesson in antibody modeling

scientific article published in November 2008

Structural elements responsible for the transition between closed states of inward rectifier K+ channel

Structure determination of a protein assembly by amino acid selective cross-saturation

scientific article published on 15 October 2010

Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces

scientific article

The Protein Data Bank archive as an open data resource

scientific article

The Protein Data Bank at 40: reflecting on the past to prepare for the future

scientific article (publication date: 7 March 2012)

The archiving and dissemination of biological structure data

scientific article

The future of the Protein Data Bank

scientific article (publication date: March 2013)

The role of charged surface residues in the binding ability of small hubs in protein-protein interaction networks

scientific article published on 21 July 2007

The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

scientific article

The zero-multipole summation method for estimating electrostatic interactions in molecular dynamics: analysis of the accuracy and application to liquid systems

scientific article published in May 2014

Validation of Structures in the Protein Data Bank

scientific article published on 21 November 2017

Variation of free-energy landscape of the p53 C-terminal domain induced by acetylation: Enhanced conformational sampling

scientific article published on 13 October 2016

Virtual states introduced for overcoming entropic barriers in conformational space

scientific article

Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking

scientific article published on 4 June 2015

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

scientific article published on 7 February 2018

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

scientific article

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

scientific article

eF-site and PDBjViewer: database and viewer for protein functional sites

scientific article published on 10 February 2004

myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme

scientific article published on 07 September 2016

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