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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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Multi-dimensional virtual system introduced to enhance canonical sampling

The Journal of chemical physics, 2017-10, Vol.147 (13), p.134102-134102

2017

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Multidimensional virtual‐system coupled canonical molecular dynamics to compute free‐energy landscapes of peptide multimer assembly

Journal of computational chemistry, 2019-10, Vol.40 (28), p.2453-2463

2019

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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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Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles

Biophysical reviews, 2022-12, Vol.14 (6), p.1423-1447

2022

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Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi-modal interaction ensemble to an auto-inhibitory state

Nucleic acids research, 2018-03, Vol.46 (5), p.2243

2018

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New Protocol for Predicting the Ligand-Binding Site and Mode Based on the 3D-RISM/KH Theory

Journal of chemical theory and computation, 2020-04, Vol.16 (4), p.2864-2876

2020

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Difference of binding modes among three ligands to a receptor mSin3B corresponding to their inhibitory activities

Scientific reports, 2021-03, Vol.11 (1), p.6178-6178, Article 6178

2021

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Multimodal Structural Distribution of the p53 C‑Terminal Domain upon Binding to S100B via a Generalized Ensemble Method: From Disorder to Extradisorder

Journal of chemical theory and computation, 2019-04, Vol.15 (4), p.2597-2607

2019

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Landscape of protein–small ligand binding modes

Protein science, 2016-09, Vol.25 (9), p.1659-1671

2016

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IBiSA_Tools: A Computational Toolkit for Ion-Binding State Analysis in Molecular Dynamics Trajectories of Ion Channels

PloS one, 2016-12, Vol.11 (12), p.e0167524-e0167524

2016

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Characteristics of interactions at protein segments without non-local intramolecular contacts in the Protein Data Bank

PloS one, 2018-12, Vol.13 (12), p.e0205052-e0205052

2018

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Studies on Molecular Dynamics of Intrinsically Disordered Proteins and Their Fuzzy Complexes: A Mini-Review

Computational and structural biotechnology journal, 2019-01, Vol.17, p.712-720

2019

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Carbon nanotube recognition by human Siglec-14 provokes inflammation

Nature nanotechnology, 2023-06, Vol.18 (6), p.628-636

2023

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Structural basis of transcription regulation by CNC family transcription factor, Nrf2

Nucleic acids research, 2022-11, Vol.50 (21), p.12543

2022

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GIANT: pattern analysis of molecular interactions in 3D structures of protein-small ligand complexes

BMC bioinformatics, 2014-01, Vol.15 (1), p.12-12, Article 12

2014

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Information quantity for secondary structure propensities of protein subsequences in the Protein Data Bank

Biophysics and Physicobiology, 2022, Vol.19, pp.e190002-1-e190002-12

2022

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Molecular Mechanisms of Functional Modulation of Transcriptional Coactivator PC4 via Phosphorylation on Its Intrinsically Disordered Region

ACS omega, 2023-04, Vol.8 (16), p.14572-14582

2023

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Molecular mechanisms of cooperative binding of transcription factors Runx1-CBFβ-Ets1 on the TCRα gene enhancer

PloS one, 2017-02, Vol.12 (2), p.e0172654-e0172654

2017

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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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mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories

Bioinformatics (Oxford, England), 2016-08, Vol.32 (16), p.2531-2533

2016

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Ion Concentration- and Voltage-Dependent Push and Pull Mechanisms of Potassium Channel Ion Conduction

PloS one, 2016-03, Vol.11 (3), p.e0150716-e0150716

2016

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Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: fly-casting mechanism

Protein engineering, design and selection, 2019-12, Vol.32 (7), p.297-308

2019

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Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking

Journal of computational chemistry, 2015-07, Vol.36 (20), p.1489-1501

2015

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Gene Cascade Finder: A tool for identification of gene cascades and its application in Caenorhabditis elegans

PloS one, 2019-09, Vol.14 (9), p.e0215187-e0215187

2019

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

Multi-dimensional virtual system introduced to enhance canonical sampling

Multidimensional virtual‐system coupled canonical molecular dynamics to compute free‐energy landscapes of peptide multimer assembly

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

Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles

Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi-modal interaction ensemble to an auto-inhibitory state

New Protocol for Predicting the Ligand-Binding Site and Mode Based on the 3D-RISM/KH Theory

Difference of binding modes among three ligands to a receptor mSin3B corresponding to their inhibitory activities

Multimodal Structural Distribution of the p53 C‑Terminal Domain upon Binding to S100B via a Generalized Ensemble Method: From Disorder to Extradisorder

Landscape of protein–small ligand binding modes

IBiSA_Tools: A Computational Toolkit for Ion-Binding State Analysis in Molecular Dynamics Trajectories of Ion Channels

Characteristics of interactions at protein segments without non-local intramolecular contacts in the Protein Data Bank

Studies on Molecular Dynamics of Intrinsically Disordered Proteins and Their Fuzzy Complexes: A Mini-Review

Carbon nanotube recognition by human Siglec-14 provokes inflammation

Structural basis of transcription regulation by CNC family transcription factor, Nrf2

GIANT: pattern analysis of molecular interactions in 3D structures of protein-small ligand complexes

Information quantity for secondary structure propensities of protein subsequences in the Protein Data Bank

Molecular Mechanisms of Functional Modulation of Transcriptional Coactivator PC4 via Phosphorylation on Its Intrinsically Disordered Region

Molecular mechanisms of cooperative binding of transcription factors Runx1-CBFβ-Ets1 on the TCRα gene enhancer

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

mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories

Ion Concentration- and Voltage-Dependent Push and Pull Mechanisms of Potassium Channel Ion Conduction

Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: fly-casting mechanism

Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking

Gene Cascade Finder: A tool for identification of gene cascades and its application in Caenorhabditis elegans

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