List of works - Shun Sakuraba

A common allosteric mechanism regulates homeostatic inactivation of auxin and gibberellin

scientific article published on 01 May 2020

A theoretical study of the two binding modes between lysozyme and tri-NAG with an explicit solvent model based on the fragment molecular orbital method ⬇️

scientific article published on February 6, 2013

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

scientific article published on 26 October 2013

Analysis of O2-binding Sites in Proteins Using Gas-Pressure NMR Spectroscopy: Outer Surface Protein A.

scientific article

Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities.

scientific article published on 19 February 2018

Comment on "Replica-exchange-with-tunneling for fast exploration of protein landscapes" [J. Chem. Phys. 143, 224102 (2015)].

scientific article published in August 2016

Critical Roles for Coiled-Coil Dimers of Butyrophilin 3A1 in the Sensing of Prenyl Pyrophosphates by Human Vγ2Vδ2 T Cells

scientific article published on 21 June 2019

Detecting coupled collective motions in protein by independent subspace analysis

scientific article published in November 2010

Distribution-function approach to free energy computation

scientific article published in September 2011

Disulfide bond formation of thiols by using carbon nanotubes.

scientific article

Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation.

scientific article published on 13 February 2018

Ermod: fast and versatile computation software for solvation free energy with approximate theory of solutions

scientific article published on 13 June 2014

Estimating Energy Parameters for RNA Secondary Structure Predictions Using Both Experimental and Computational Data

scientific article published on 12 March 2018

Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation

scientific article published on 01 December 2012

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

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

scientific article published on 17 October 2019

Interaction of naphthalene derivatives with lipids in membranes studied by the 1H-nuclear Overhauser effect and molecular dynamics simulation

scientific article published on 17 September 2012

Molecular binding sites are located near the interface of intrinsic dynamics domains (IDDs).

scientific article

Multiple Markov transition matrix method: obtaining the stationary probability distribution from multiple simulations

scientific article

NMR-NOE and MD simulation study on phospholipid membranes: dependence on membrane diameter and multiple time scale dynamics

scientific article published on 05 July 2011

Nuclear magnetic resonance-based determination of dioxygen binding sites in protein cavities.

scientific article published on 22 December 2017

Performance evaluation of the zero-multipole summation method in modern molecular dynamics software

scientific article published on 04 May 2018

Predicting RNA Duplex Dimerization Free-Energy Changes upon Mutations Using Molecular Dynamics Simulations.

scientific article published on 20 October 2015

Role of the Photosystem II as an Environment in the Oxidation Free Energy of the Mn Cluster from S1 to S2

scientific article published on 19 July 2019

Salt-dependent elution of uncharged aromatic solutes in ion-exchange chromatography

scientific article published on 6 March 2018

Short synthesis of (+)-cylindricine C by using a catalytic asymmetric Michael reaction with a two-center organocatalyst

scientific article published on 01 July 2006

Spotting the difference in molecular dynamics simulations of biomolecules

scientific article published on August 2016

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

The binding affinity of uncharged aromatic solutes for negatively charged resins is enhanced by cations via cation-π interactions: The case of sodium ion and arginine

scientific article published on 21 February 2019

List of works by Shun Sakuraba

A common allosteric mechanism regulates homeostatic inactivation of auxin and gibberellin

A theoretical study of the two binding modes between lysozyme and tri-NAG with an explicit solvent model based on the fragment molecular orbital method ⬇️

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

Analysis of O2-binding Sites in Proteins Using Gas-Pressure NMR Spectroscopy: Outer Surface Protein A.

Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities.

Comment on "Replica-exchange-with-tunneling for fast exploration of protein landscapes" [J. Chem. Phys. 143, 224102 (2015)].

Critical Roles for Coiled-Coil Dimers of Butyrophilin 3A1 in the Sensing of Prenyl Pyrophosphates by Human Vγ2Vδ2 T Cells

Detecting coupled collective motions in protein by independent subspace analysis

Distribution-function approach to free energy computation

Disulfide bond formation of thiols by using carbon nanotubes.

Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation.

Ermod: fast and versatile computation software for solvation free energy with approximate theory of solutions

Estimating Energy Parameters for RNA Secondary Structure Predictions Using Both Experimental and Computational Data

Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation

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

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

Interaction of naphthalene derivatives with lipids in membranes studied by the 1H-nuclear Overhauser effect and molecular dynamics simulation

Molecular binding sites are located near the interface of intrinsic dynamics domains (IDDs).

Multiple Markov transition matrix method: obtaining the stationary probability distribution from multiple simulations

NMR-NOE and MD simulation study on phospholipid membranes: dependence on membrane diameter and multiple time scale dynamics

Nuclear magnetic resonance-based determination of dioxygen binding sites in protein cavities.

Performance evaluation of the zero-multipole summation method in modern molecular dynamics software

Predicting RNA Duplex Dimerization Free-Energy Changes upon Mutations Using Molecular Dynamics Simulations.

Role of the Photosystem II as an Environment in the Oxidation Free Energy of the Mn Cluster from S1 to S2

Salt-dependent elution of uncharged aromatic solutes in ion-exchange chromatography

Short synthesis of (+)-cylindricine C by using a catalytic asymmetric Michael reaction with a two-center organocatalyst

Spotting the difference in molecular dynamics simulations of biomolecules

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

The binding affinity of uncharged aromatic solutes for negatively charged resins is enhanced by cations via cation-π interactions: The case of sodium ion and arginine