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Molecular dynamics simulations for the protein–ligand complex structures obtained by computational docking studies using implicit or explicit solvents

Chemical physics letters, 2021-10, Vol.781, p.139022, Article 139022

2021

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Mechanisms of Deamidation of Asparagine Residues and Effects of Main-Chain Conformation on Activation Energy

International journal of molecular sciences, 2020-10, Vol.21 (19), p.7035

2020

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Theoretical Studies on the Effect of Isomerized Aspartic Acid Residues on the Three-Dimensional Structures of Bovine Pancreatic Ribonucleases A

Biological and Pharmaceutical Bulletin, 2021/07/01, Vol.44(7), pp.967-975

2021

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Computational Estimation of Residues Involving Resistance to the SARS-CoV-2 Main Protease Inhibitor Ensitrelvir Based on Virtual Alanine Scan of the Active Site

Biological and Pharmaceutical Bulletin, 2024/05/17, Vol.47(5), pp.967-977

2024

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Modification of the pH Dependence of Assembly of Yeast Cargo Receptor Emp47p Coiled-Coil Domains: Computational Design and Experimental Mutagenesis

The journal of physical chemistry. B, 2021-03, Vol.125 (9), p.2222-2230

2021

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Possible Mechanisms of Nonenzymatic Formation of Dehydroalanine Residue Catalyzed by Dihydrogen Phosphate Ion

The journal of physical chemistry. B, 2019-04, Vol.123 (15), p.3147-3155

2019

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Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2

International journal of molecular sciences, 2021-09, Vol.22 (18), p.9837

2021

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Structural Impact Assessment of Cytochrome P450 2A13 Polymorphisms Using Molecular Dynamics Simulations

Biological and Pharmaceutical Bulletin, 2024/03/13, Vol.47(3), pp.620-628

2024

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Development of Force Field Parameters for p-Carborane to Investigate the Structural Influence of Carborane Derivatives on Drug Targets by Complex Formation

Biological and Pharmaceutical Bulletin, 2020/12/01, Vol.43(12), pp.1931-1939

2020

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Computational studies on nonenzymatic pyroglutamylation mechanism of N-terminal glutamic acid residues in aqueous conditions

Molecular physics, 2020-07, Vol.118 (14), p.e1702727

2020

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Three dimensional structures of putative, primitive proteins to investigate the origin of homochirality

Scientific reports, 2019-08, Vol.9 (1), p.11594-8, Article 11594

2019

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Structural investigation of pathogenic variants in dihydropyrimidinase using molecular dynamics simulations

Journal of molecular graphics & modelling, 2022-12, Vol.117, p.108288, Article 108288

2022

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Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins

Molecules (Basel, Switzerland), 2017-10, Vol.22 (10), p.1716

2017

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Computational quantitation of the aldehyde forms of aldohexoses and disaccharides composed of d-glucose: Predictions of their reactivities in the Maillard reaction

Computational and theoretical chemistry, 2022-03, Vol.1209, p.113605, Article 113605

2022

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Effects of substituent pattern on the intracellular target of antiproliferative benzo[b]thiophenyl chromone derivatives

European journal of medicinal chemistry, 2021-10, Vol.222, p.113578-113578, Article 113578

2021

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Effect of the Addition of the Fifth Amino Acid to [GADV]-Protein on the Three-Dimensional Structure

Life (Basel, Switzerland), 2023-01, Vol.13 (1), p.246

2023

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Influences of conformations of peptides on stereoinversions and/or isomerizations of aspartic acid residues

Biochimica et biophysica acta. Proteins and proteomics, 2018-07, Vol.1866 (7), p.783-788

2018

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Molecular Mechanisms of Succinimide Formation from Aspartic Acid Residues Catalyzed by Two Water Molecules in the Aqueous Phase

International journal of molecular sciences, 2021-01, Vol.22 (2), p.509

2021

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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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Functional Characterization of 12 Dihydropyrimidinase Allelic Variants in Japanese Individuals for the Prediction of 5-Fluorouracil Treatment-Related Toxicity

Drug metabolism and disposition, 2023-02, Vol.51 (2), p.165-173

2023

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Theoretical study on keto-enol tautomerisation of glutarimide for exploration of the isomerisation reaction pathway of glutamic acid in proteins using density functional theory

Molecular physics, 2017-03, Vol.115 (5), p.560-565

2017

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Deciphering Structural Alterations Associated with Activity Reductions of Genetic Polymorphisms in Cytochrome P450 2A6 Using Molecular Dynamics Simulations

International journal of molecular sciences, 2021-09, Vol.22 (18), p.10119

2021

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CYP2D6 genotyping analysis and functional characterization of novel allelic variants in a Ni-Vanuatu and Kenyan population by assessing dextromethorphan O-demethylation activity

Drug metabolism and pharmacokinetics, 2020-02, Vol.35 (1), p.89-101

2020

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Computational Studies on Water-Catalyzed Mechanisms for Stereoinversion of Glutarimide Intermediates Formed from Glutamic Acid Residues in Aqueous Phase

International journal of molecular sciences, 2019-05, Vol.20 (10), p.2410

2019

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Computational Studies on the Nonenzymatic Deamidation Mechanisms of Glutamine Residues

ACS omega, 2019-02, Vol.4 (2), p.3508-3513

2019

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Molecular dynamics simulations for the protein–ligand complex structures obtained by computational docking studies using implicit or explicit solvents

Mechanisms of Deamidation of Asparagine Residues and Effects of Main-Chain Conformation on Activation Energy

Theoretical Studies on the Effect of Isomerized Aspartic Acid Residues on the Three-Dimensional Structures of Bovine Pancreatic Ribonucleases A

Computational Estimation of Residues Involving Resistance to the SARS-CoV-2 Main Protease Inhibitor Ensitrelvir Based on Virtual Alanine Scan of the Active Site

Modification of the pH Dependence of Assembly of Yeast Cargo Receptor Emp47p Coiled-Coil Domains: Computational Design and Experimental Mutagenesis

Possible Mechanisms of Nonenzymatic Formation of Dehydroalanine Residue Catalyzed by Dihydrogen Phosphate Ion

Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2

Structural Impact Assessment of Cytochrome P450 2A13 Polymorphisms Using Molecular Dynamics Simulations

Development of Force Field Parameters for p-Carborane to Investigate the Structural Influence of Carborane Derivatives on Drug Targets by Complex Formation

Computational studies on nonenzymatic pyroglutamylation mechanism of N-terminal glutamic acid residues in aqueous conditions

Three dimensional structures of putative, primitive proteins to investigate the origin of homochirality

Structural investigation of pathogenic variants in dihydropyrimidinase using molecular dynamics simulations

Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins

Computational quantitation of the aldehyde forms of aldohexoses and disaccharides composed of d-glucose: Predictions of their reactivities in the Maillard reaction

Effects of substituent pattern on the intracellular target of antiproliferative benzo[b]thiophenyl chromone derivatives

Effect of the Addition of the Fifth Amino Acid to [GADV]-Protein on the Three-Dimensional Structure

Influences of conformations of peptides on stereoinversions and/or isomerizations of aspartic acid residues

Molecular Mechanisms of Succinimide Formation from Aspartic Acid Residues Catalyzed by Two Water Molecules in the Aqueous Phase

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

Functional Characterization of 12 Dihydropyrimidinase Allelic Variants in Japanese Individuals for the Prediction of 5-Fluorouracil Treatment-Related Toxicity

Theoretical study on keto-enol tautomerisation of glutarimide for exploration of the isomerisation reaction pathway of glutamic acid in proteins using density functional theory

Deciphering Structural Alterations Associated with Activity Reductions of Genetic Polymorphisms in Cytochrome P450 2A6 Using Molecular Dynamics Simulations

CYP2D6 genotyping analysis and functional characterization of novel allelic variants in a Ni-Vanuatu and Kenyan population by assessing dextromethorphan O-demethylation activity

Computational Studies on Water-Catalyzed Mechanisms for Stereoinversion of Glutarimide Intermediates Formed from Glutamic Acid Residues in Aqueous Phase

Computational Studies on the Nonenzymatic Deamidation Mechanisms of Glutamine Residues

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