List of works - Naoto Hori

A Coarse-Grained Simulation Study of Ribosome and tRNA Dynamics during Translocation

scientific article published in January 2012

Biomolecular Coarse-Grained Simulation Program CafeMol

article published in 2010

CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work

scientific article published on 19 May 2011

Coarse-Grained Structure-Based Model for RNA-Protein Complexes Developed by Fluctuation Matching

article

Competition between Stacking and Divalent Cation-Mediated Electrostatic Interactions Determines the Conformations of Short DNA Sequences

scientific article published on 18 March 2024

Condensates in RNA Repeat Sequences are Heterogeneously Organized and Exhibit Reptation-like Dynamics

preprint dated 21 February 2021

Condensates in RNA Repeat Sequences are Heterogeneously Organized and Exhibit Reptation-like Dynamics

preprint dated 31 March 2021

Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics

scientific article published on 2 May 2022

Folding RNA in mixtures of monovalent and divalent cations: Theory and simulations

scientific article published on 12 August 2019

Folding energy landscape and network dynamics of small globular proteins

scientific article

Frictional Effects on RNA Folding: Speed Limit and Kramers Turnover

scientific article published on 18 September 2018

Frictional effects on RNA folding: Speed limit and Kramers turnover

How Co-translational Folding of Multi-domain Protein Is Affected by Elongation Schedule: Molecular Simulations

scientific article published on 9 July 2015

Ion Condensation onto Ribozyme Is Site Specific and Fold Dependent

scientific article published on 11 May 2019

Ion Condensation onto Ribozyme is Site-Specific and Fold-Dependent

scientific article published on 15 February 2019

Mechanical Force and Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot

scientific article published in February 2016

Molecular Simulations of Ion Effects on the Thermodynamics of RNA Folding

scientific article published on 05 December 2018

Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot

article published in the Proceedings of the National Academy of Sciences of the United States of America

Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot

preprint dated 19 October 2017

Multiscale methods for protein folding simulations

scientific article published on 29 April 2010

Multistep Folding Kinetics of Group I Intron RNA Studied by Mg 2+ -Concentration Jump Simulations

scientific article published in February 2017

Odd-even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation

scientific article published on 9 January 2023

Odd-even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation

scientific article published on 13 June 2023

Protein collapse is encoded in the folded state architecture.

scientific article published on 27 April 2017

Recognize Online Handwritten Bangla Characters Using Hausdorff Distance-Based Feature

scientific article published in 2017

Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension ⬇️

scientific article published on 14 June 2016

Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension

scientific article published on 15 April 2016

Salt-Dependent Self-Association of Trinucleotide Repeat RNA Sequences

scientific article published in April 2024

Salt-dependent self-association of trinucleotide repeat RNA sequences

scientific article published on 27 November 2023

Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA

scientific article published on 26 June 2018

Sequence-dependent Three Interaction Site (TIS) Model for Single and Double-stranded DNA

preprint

Shape changes and cooperativity in the folding of central domain of the 16S ribosomal RNA

scientific article published on 9 April 2020

Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA

scientific article published on 9 March 2021

Theory and simulations for RNA folding in mixtures of monovalent and divalent cations

scientific article published on 30 September 2019

Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and topological frustration one molecule at a time

preprint dated 6 February 2023

Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and topological frustration one molecule at a time

scientific article published on 27 October 2023

List of works by Naoto Hori

A Coarse-Grained Simulation Study of Ribosome and tRNA Dynamics during Translocation

Biomolecular Coarse-Grained Simulation Program CafeMol

CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work

Coarse-Grained Structure-Based Model for RNA-Protein Complexes Developed by Fluctuation Matching

Competition between Stacking and Divalent Cation-Mediated Electrostatic Interactions Determines the Conformations of Short DNA Sequences

Condensates in RNA Repeat Sequences are Heterogeneously Organized and Exhibit Reptation-like Dynamics

Condensates in RNA Repeat Sequences are Heterogeneously Organized and Exhibit Reptation-like Dynamics

Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics

Folding RNA in mixtures of monovalent and divalent cations: Theory and simulations

Folding energy landscape and network dynamics of small globular proteins

Frictional Effects on RNA Folding: Speed Limit and Kramers Turnover

Frictional effects on RNA folding: Speed limit and Kramers turnover

How Co-translational Folding of Multi-domain Protein Is Affected by Elongation Schedule: Molecular Simulations

Ion Condensation onto Ribozyme Is Site Specific and Fold Dependent

Ion Condensation onto Ribozyme is Site-Specific and Fold-Dependent

Mechanical Force and Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot

Molecular Simulations of Ion Effects on the Thermodynamics of RNA Folding

Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot

Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot

Multiscale methods for protein folding simulations

Multistep Folding Kinetics of Group I Intron RNA Studied by Mg 2+ -Concentration Jump Simulations

Odd-even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation

Odd-even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation

Protein collapse is encoded in the folded state architecture.

Recognize Online Handwritten Bangla Characters Using Hausdorff Distance-Based Feature

Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension ⬇️

Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension

Salt-Dependent Self-Association of Trinucleotide Repeat RNA Sequences

Salt-dependent self-association of trinucleotide repeat RNA sequences

Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA

Sequence-dependent Three Interaction Site (TIS) Model for Single and Double-stranded DNA

Shape changes and cooperativity in the folding of central domain of the 16S ribosomal RNA

Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA

Theory and simulations for RNA folding in mixtures of monovalent and divalent cations

Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and topological frustration one molecule at a time

Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and topological frustration one molecule at a time