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Unraveling Binding Mechanism and Stability of Urease Inhibitors: A QM/MM MD Study

Molecules (Basel, Switzerland), 2023-03, Vol.28 (6), p.2697

2023

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Transition State Search Using rPM6: Iron- and Manganese-Catalyzed Oxidation Reactions as a Test Case

Bulletin of the Chemical Society of Japan, 2018-09, Vol.91 (9), p.1377-1389

2018

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Density functional study of porphyrin distortion effects on redox potential of heme

Journal of computational chemistry, 2018-01, Vol.39 (3), p.143-150

2018

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Computational Exploration of Minimum Energy Reaction Pathway of N2O Formation from Intermediate I of P450nor Using an Active Center Model

International journal of molecular sciences, 2023-12, Vol.24 (24), p.17172

2023

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Depolarizing Effects in Hydrogen Bond Energy in 310-Helices Revealed by Quantum Chemical Analysis

International journal of molecular sciences, 2022-08, Vol.23 (16), p.9032

2022

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rPM6 Parameters for Manganese and Application to Transition State Search for Oxidation Reactions of Cyclohexene by Manganese(IV)-Oxo Species

Chemistry letters, 2017-10, Vol.46 (10), p.1567-1569

2017

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Development of a one-step analysis method for several amino acids using a microfluidic paper-based analytical device

Scientific reports, 2022-03, Vol.12 (1), p.3427-3427, Article 3427

2022

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Random Forest Classifier of Heme Proteins Using Porphyrin Distortions and Axial Ligands of Heme

Chemistry letters, 2023-06, Vol.52 (6), p.503-507

2023

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Protein folding pathways extracted by OFLOOD: Outlier FLOODing method

Journal of computational chemistry, 2015-01, Vol.36 (2), p.97-102

2015

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Global Analysis of Heme Proteins Elucidates the Correlation between Heme Distortion and the Heme-Binding Pocket

Journal of chemical information and modeling, 2022-02, Vol.62 (4), p.775-784

2022

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PyDISH: database and analysis tools for heme porphyrin distortion in heme proteins

Database : the journal of biological databases and curation, 2023-12, Vol.2023

2023

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Quantum chemical studies on hydrogen bonds in helical secondary structures

Biophysical reviews, 2022-12, Vol.14 (6), p.1369-1378

2022

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Analysis of Fluctuation in the Heme-Binding Pocket and Heme Distortion in Hemoglobin and Myoglobin

Life (Basel, Switzerland), 2022-01, Vol.12 (2), p.210

2022

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Common folding processes of mini‐proteins: Partial formations of secondary structures initiate the immediate protein folding

Journal of computational chemistry, 2017-04, Vol.38 (11), p.790-797

2017

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Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: Application to the folding of a mini-protein, chignolin

Journal of computational chemistry, 2015-04, Vol.36 (10), p.763-772

2015

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Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate

Nature communications, 2017-11, Vol.8 (1), p.1585-9, Article 1585

2017

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Quantitative Assessment of rPM6 for Fluorine- and Chlorine-Containing Metal Complexes: Comparison with Experimental, First-Principles, and Other Semiempirical Results

Molecules (Basel, Switzerland), 2018-12, Vol.23 (12), p.3332

2018

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Effects of Active-Center Reduction of Plant-Type Ferredoxin on Its Structure and Dynamics: Computational Analysis Using Molecular Dynamics Simulations

International journal of molecular sciences, 2022-12, Vol.23 (24), p.15913

2022

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Zn2+-Binding to the Voltage-Gated Proton Channel Hv1/VSOP

The journal of physical chemistry. B, 2018-10, Vol.122 (39), p.9076-9080

2018

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Development of massive multilevel molecular dynamics simulation program, platypus (PLATform for dYnamic protein unified simulation), for the elucidation of protein functions

Journal of computational chemistry, 2016-05, Vol.37 (12), p.1125-1132

2016

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Inverse Ubbelohde effect in the short hydrogen bond of photosystem II: Relation between H/D isotope effect and symmetry in potential energy profile

Journal of computational chemistry, 2016-09, Vol.37 (23), p.2140-2145

2016

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QM/MM Molecular Dynamics Simulations Revealed Catalytic Mechanism of Urease

The journal of physical chemistry. B, 2022-03, Vol.126 (10), p.2087-2097

2022

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Direct Interaction between the Voltage Sensors Produces Cooperative Sustained Deactivation in Voltage-gated H+ Channel Dimers

The Journal of biological chemistry, 2016-03, Vol.291 (11), p.5935-5947

2016

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Conformational Preference of Flavonols and Its Effect on the Chemical Properties Involved in Radical Scavenging Activity

Chemistry an international journal, 2022-09, Vol.4 (4), p.1123-1135

2022

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Highly Sensitive Colorimetric Detection of Histidine Using Histidyl-tRNA Synthetase as the Bioreceptor

Biomedical Materials & Devices, 2023-09, Vol.1 (2), p.1022-1027

2023

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Unraveling Binding Mechanism and Stability of Urease Inhibitors: A QM/MM MD Study

Transition State Search Using rPM6: Iron- and Manganese-Catalyzed Oxidation Reactions as a Test Case

Density functional study of porphyrin distortion effects on redox potential of heme

Computational Exploration of Minimum Energy Reaction Pathway of N2O Formation from Intermediate I of P450nor Using an Active Center Model

Depolarizing Effects in Hydrogen Bond Energy in 310-Helices Revealed by Quantum Chemical Analysis

rPM6 Parameters for Manganese and Application to Transition State Search for Oxidation Reactions of Cyclohexene by Manganese(IV)-Oxo Species

Development of a one-step analysis method for several amino acids using a microfluidic paper-based analytical device

Random Forest Classifier of Heme Proteins Using Porphyrin Distortions and Axial Ligands of Heme

Protein folding pathways extracted by OFLOOD: Outlier FLOODing method

Global Analysis of Heme Proteins Elucidates the Correlation between Heme Distortion and the Heme-Binding Pocket

PyDISH: database and analysis tools for heme porphyrin distortion in heme proteins

Quantum chemical studies on hydrogen bonds in helical secondary structures

Analysis of Fluctuation in the Heme-Binding Pocket and Heme Distortion in Hemoglobin and Myoglobin

Common folding processes of mini‐proteins: Partial formations of secondary structures initiate the immediate protein folding

Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: Application to the folding of a mini-protein, chignolin

Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate

Quantitative Assessment of rPM6 for Fluorine- and Chlorine-Containing Metal Complexes: Comparison with Experimental, First-Principles, and Other Semiempirical Results

Effects of Active-Center Reduction of Plant-Type Ferredoxin on Its Structure and Dynamics: Computational Analysis Using Molecular Dynamics Simulations

Zn2+-Binding to the Voltage-Gated Proton Channel Hv1/VSOP

Development of massive multilevel molecular dynamics simulation program, platypus (PLATform for dYnamic protein unified simulation), for the elucidation of protein functions

Inverse Ubbelohde effect in the short hydrogen bond of photosystem II: Relation between H/D isotope effect and symmetry in potential energy profile

QM/MM Molecular Dynamics Simulations Revealed Catalytic Mechanism of Urease

Direct Interaction between the Voltage Sensors Produces Cooperative Sustained Deactivation in Voltage-gated H+ Channel Dimers

Conformational Preference of Flavonols and Its Effect on the Chemical Properties Involved in Radical Scavenging Activity

Highly Sensitive Colorimetric Detection of Histidine Using Histidyl-tRNA Synthetase as the Bioreceptor

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