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

The Journal of chemical physics, 2016-08, Vol.145 (5), p.057101-057101

Sakuraba, Shun

2016

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

PLoS computational biology, 2022-01, Vol.18 (1), p.e1009804-e1009804

2022

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

Nature communications, 2021-11, Vol.12 (1), p.6605-10, Article 6605

2021

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Large-Scale Parallel Implementation of Hartree–Fock Exchange Energy on Real-Space Grids Using 3D-Parallel Fast Fourier Transform

Journal of chemical information and modeling, 2020-03, Vol.60 (3), p.1376-1389

2020

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

Journal of computational chemistry, 2018-07, Vol.39 (20), p.1551-1560

2018

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

PLoS computational biology, 2016-03, Vol.12 (3), p.e1004788-e1004788

2016

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A common allosteric mechanism regulates homeostatic inactivation of auxin and gibberellin

Nature communications, 2020-05, Vol.11 (1), p.2143-2143, Article 2143

2020

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Interaction-component analysis of the hydration and urea effects on cytochrome c

The Journal of chemical physics, 2016-02, Vol.144 (8), p.085102-085102

2016

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

The journal of physical chemistry. B, 2018-03, Vol.122 (9), p.2495-2503

2018

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

Nature communications, 2019-10, Vol.10 (1), p.4724-13, Article 4724

2019

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

PLoS computational biology, 2018-03, Vol.14 (3), p.e1006024-e1006024

2018

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

The journal of physical chemistry. B, 2019-08, Vol.123 (33), p.7081-7091

2019

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FEP suite: A simulation pipeline for the free-energy calculation of biomolecules

Biophysical journal, 2024-02, Vol.123 (3), p.423a-424a

Sakuraba, Shun

2024

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Spotting the difference in molecular dynamics simulations of biomolecules

The Journal of chemical physics, 2016-08, Vol.145 (7), p.074116-074116

2016

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

PLoS computational biology, 2019-10, Vol.15 (10), p.e1007439-e1007439

2019

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

BMC bioinformatics, 2018-02, Vol.19 (Suppl 1), p.38-38, Article 38

2018

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

The journal of physical chemistry letters, 2015-11, Vol.6 (21), p.4348-4351

2015

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Free energy profile for unwrapping outer superhelical turn of CENP-A nucleosome

Biophysics and Physicobiology, 2019, Vol.16, pp.337-343

2019

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Fly casting with ligand sliding and orientational selection supporting complex formation of a GPCR and a middle sized flexible molecule

Scientific reports, 2022-08, Vol.12 (1), p.13792-13792, Article 13792

2022

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

IEEE/ACM transactions on computational biology and bioinformatics, 2019-09, Vol.16 (5), p.1645-1655

2019

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A Computational Study of Free-Energy Changes Upon Protein Mutations

Biophysical journal, 2020-02, Vol.118 (3), p.144a-144a

Sakuraba, Shun

2020

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HNF1A POU Domain Mutations Found in Japanese Liver Cancer Patients Cause Downregulation of HNF4A Promoter Activity with Possible Disruption in Transcription Networks

Genes, 2022-02, Vol.13 (3), p.413

2022

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Free-Energy Calculation of Ribonucleic Inosines and Its Application to Nearest-Neighbor Parameters

Journal of chemical theory and computation, 2020-09, Vol.16 (9), p.5923-5935

2020

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

Journal of computational chemistry, 2014-01, Vol.35 (1), p.39-50

2014

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Analysis of O 2 -binding Sites in Proteins Using Gas-Pressure NMR Spectroscopy: Outer Surface Protein A

Biophysical journal, 2017-05, Vol.112 (9), p.1820-1828

2017

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

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

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

Large-Scale Parallel Implementation of Hartree–Fock Exchange Energy on Real-Space Grids Using 3D-Parallel Fast Fourier Transform

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

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

A common allosteric mechanism regulates homeostatic inactivation of auxin and gibberellin

Interaction-component analysis of the hydration and urea effects on cytochrome c

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

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

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

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

FEP suite: A simulation pipeline for the free-energy calculation of biomolecules

Spotting the difference in molecular dynamics simulations of biomolecules

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

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

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

Free energy profile for unwrapping outer superhelical turn of CENP-A nucleosome

Fly casting with ligand sliding and orientational selection supporting complex formation of a GPCR and a middle sized flexible molecule

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

A Computational Study of Free-Energy Changes Upon Protein Mutations

HNF1A POU Domain Mutations Found in Japanese Liver Cancer Patients Cause Downregulation of HNF4A Promoter Activity with Possible Disruption in Transcription Networks

Free-Energy Calculation of Ribonucleic Inosines and Its Application to Nearest-Neighbor Parameters

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

Analysis of O 2 -binding Sites in Proteins Using Gas-Pressure NMR Spectroscopy: Outer Surface Protein A

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