Lista de obras - Hidetoshi Kono - Dominio Público Uruguay

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

artículo científico publicado en 2009

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

artículo científico publicado en 2017

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

artículo científico publicado en 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.

artículo científico publicado en 2012

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

artículo científico publicado en 2008

Covalent Modifications of Histone H3K9 Promote Binding of CHD3.

artículo científico publicado en 2017

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

artículo científico publicado en 2017

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

artículo científico publicado en 2017

De novo design of a redox-active minimal rubredoxin mimic

artículo científico publicado en 2005

Distinct Roles of Histone H3 and H2A Tails in Nucleosome Stability

artículo científico publicado en 2016

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.

artículo científico publicado en 1994

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

artículo científico publicado en 2022

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

artículo científico publicado en 2018

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

artículo científico publicado en 2016

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

artículo científico publicado en 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

artículo científico publicado en 2002

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

artículo científico publicado en 2000

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

artículo científico publicado en 2005

Intermolecular and intramolecular readout mechanisms in protein-DNA recognition.

artículo científico publicado en 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

artículo científico publicado en 2013

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

artículo científico publicado en 2014

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

artículo científico publicado en 2018

Phase retrieval from single biomolecule diffraction pattern

artículo científico publicado en 2012

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

artículo científico publicado en 2017

ProTherm: Thermodynamic Database for Proteins and Mutants.

artículo científico publicado en 1999

Protein-DNA recognition patterns and predictions.

artículo científico publicado en 2005

Rational design of DNA sequence-specific zinc fingers.

artículo científico publicado en 2012

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

artículo científico publicado en 2006

Relationship between amino acid properties and protein stability: buried mutations

artículo científico publicado en 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.

artículo científico publicado en 2009

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

artículo científico publicado en 2016

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

artículo científico publicado en 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

artículo científico publicado en 2021

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

artículo científico publicado en 2001

Thermodynamic databases for proteins and protein-nucleic acid interactions.

artículo científico publicado en 2001

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

artículo científico publicado en 2015

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

artículo científico publicado en 2011

coliSNP database server mapping nsSNPs on protein structures.

artículo científico publicado en 2007

Lista de obras de Hidetoshi Kono

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

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

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

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

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.

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

Covalent Modifications of Histone H3K9 Promote Binding of CHD3.

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

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

De novo design of a redox-active minimal rubredoxin mimic

Distinct Roles of Histone H3 and H2A Tails in Nucleosome Stability

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

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

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

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

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

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

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

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

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

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

Intermolecular and intramolecular readout mechanisms in protein-DNA recognition.

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

Local conformational changes in the DNA interfaces of proteins

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

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

Phase retrieval from single biomolecule diffraction pattern

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

ProTherm: Thermodynamic Database for Proteins and Mutants.

Protein-DNA recognition patterns and predictions.

Rational design of DNA sequence-specific zinc fingers.

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

Relationship between amino acid properties and protein stability: buried mutations

Role of inter and intramolecular interactions in protein-DNA recognition

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

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

Spotting the difference in molecular dynamics simulations of biomolecules

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

Structural basis for designing an array of engrailed homeodomains

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

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

Thermodynamic databases for proteins and protein-nucleic acid interactions.

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

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

coliSNP database server mapping nsSNPs on protein structures.