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List of works by Hidetoshi Kono

A generalized conformational energy function of DNA derived from molecular dynamics simulations.

scientific article published on 3 September 2009

A new method for evaluating the specificity of indirect readout in protein–DNA recognition ⬇️

scientific article published on May 22, 2012

Accessibility of the histone H3 tail in the nucleosome for binding of paired readers.

scientific article published on 14 November 2017

Adaptive lambda square dynamics simulation: an efficient conformational sampling method for biomolecules.

scientific article published on 26 October 2013

Balance between DNA-binding affinity and specificity enables selective recognition of longer target sequences in vivo

scientific article published on 06 August 2019

Classifying and assembling two-dimensional X-ray laser diffraction patterns of a single particle to reconstruct the three-dimensional diffraction intensity function: resolution limit due to the quantum noise.

scientific article published on 22 March 2012

Comparison of DNA hydration patterns obtained using two distinct computational methods, molecular dynamics simulation and three-dimensional reference interaction site model theory.

scientific article published in May 2008

Covalent Modifications of Histone H3K9 Promote Binding of CHD3.

scientific article published on October 2017

Crystal structure of the overlapping dinucleosome composed of hexasome and octasome.

scientific article published in April 2017

DNA conformational transitions inferred from re-evaluation of m|Fo| - D|Fc| electron-density maps

scientific article

De novo design of a redox-active minimal rubredoxin mimic

scientific article

Dissociation Free-Energy Profiles of Specific and Nonspecific DNA–Protein Complexes ⬇️

scientific article published on June 11, 2013

Distinct Roles of Histone H3 and H2A Tails in Nucleosome Stability

scientific article

Emerging BRAF Mutations in Cancer Progression and Their Possible Effects on Transcriptional Networks

scientific article published on 12 November 2020

Energy minimization method using automata network for sequence and side-chain conformation prediction from given backbone geometry.

scientific article

Extended ensemble simulations of a SARS-CoV-2 nsp1-5'-UTR complex

scientific article published on 19 January 2022

Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA.

scientific article published on 5 March 2018

H3 Histone Tail Conformation within the Nucleosome and the Impact of K14 Acetylation Studied Using Enhanced Sampling Simulation

scientific article

H4 Tails Potentially Produce the Diversity in the Orientation of Two Nucleosomes.

scientific article published in September 2017

Histone H3K23-specific acetylation by MORF is coupled to H3K14 acylation

scientific article published on 17 October 2019

Importance of mutant position in Ramachandran plot for predicting protein stability of surface mutations

scientific article published on 01 August 2002

Importance of surrounding residues for protein stability of partially buried mutations.

scientific article published in October 2000

Integration of bioinformatics and computational biology to understand protein-DNA recognition mechanism

scientific article published on 01 February 2005

Intermolecular and intramolecular readout mechanisms in protein-DNA recognition.

scientific article published in March 2004

Investigating the Influence of Arginine Dimethylation on Nucleosome Dynamics Using All-Atom Simulations and Kinetic Analysis

article

Local conformational changes in the DNA interfaces of proteins

scientific article

Local dynamics coupled to hydration water determines DNA-sequence-dependent deformability

scientific article published on 29 August 2014

Loss-of-function mutations in Zn-finger DNA-binding domain of HNF4A cause aberrant transcriptional regulation in liver cancer.

scientific article published on 25 May 2018

Molecular Structure of Isolated MvspI, a Variable Surface Protein of the Fish Pathogen Mycoplasma mobile ⬇️

scientific article published on March 23, 2012

Phase retrieval from single biomolecule diffraction pattern ⬇️

scientific article published on February 13, 2012

Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences.

scientific article

ProTherm: Thermodynamic Database for Proteins and Mutants.

scientific article published on January 1999

Protein-DNA recognition patterns and predictions.

scientific article

Rational design of DNA sequence-specific zinc fingers.

scientific article published on 23 February 2012

ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition

scientific article published on July 2006

Relationship between amino acid properties and protein stability: buried mutations

scientific article published on 01 July 1999

Role of inter and intramolecular interactions in protein-DNA recognition

scientific article published on 24 October 2005

Sequence dependencies of DNA deformability and hydration in the minor groove.

scientific article

Sequence-Dependent Conformational Energy of DNA Derived from Molecular Dynamics Simulations: Toward Understanding the Indirect Readout Mechanism in Protein−DNA Recognition

article

Spotting the difference in molecular dynamics simulations of biomolecules

scientific article published on August 2016

Stability analysis for the cavity-filling mutations of the Myb DNA-binding domain utilizing free-energy calculations

scientific article published on 01 February 2000

Structural basis for designing an array of engrailed homeodomains

scientific article published on 17 August 2020

Structural basis of the regulation of the normal and oncogenic methylation of nucleosomal histone H3 Lys36 by NSD2

scientific article published on 15 November 2021

Thermodynamic database for protein-nucleic acid interactions (ProNIT).

scientific article published in November 2001

Thermodynamic databases for proteins and protein-nucleic acid interactions.

scientific article

Two arginine residues suppress the flexibility of nucleosomal DNA in the canonical nucleosome core

scientific article (publication date: 2015)

What determines water-bridge lifetimes at the surface of DNA? Insight from systematic molecular dynamics analysis of water kinetics for various DNA sequences

scientific article published on 25 September 2011

coliSNP database server mapping nsSNPs on protein structures.

scientific article

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