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Dynamical Cooperativity of Ligand-Residue Interactions Evaluated with the Fragment Molecular Orbital Method

Shigenori Tanaka, Shusuke Tokutomi, Ryo Hatada,, Koji Okuwaki, Kazuki Akisawa, Kaori Fukuzawa, Yuto Komeiji, Yoshio Okiyama, Yuji Mochizuki

Version 1 posted 10 February 2021

350

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Chemical Education

Working Paper

Reduction of Orbital Space for Molecular Orbital Calculations with Quantum Computation Simulator for Educations

Yuji Mochizuki, Koji Okuwaki, Takumi Kato, Yuichiro Minato

Version 1 posted 24 September 2019

787

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1

Citations

Biological and Medicinal Chemistry

Working Paper

Fragment Molecular Orbital Based Interaction Analyses on Complexes Between RBD Variants and ACE2

Kazuki Akisawa, Ryo Hatada, Koji Okuwaki, Shun Kitahara, Yusuke Tachino, Yuji Mochizuki

Version 2 posted 30 March 2021

445

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Theoretical and Computational Chemistry

Working Paper

Interaction Analyses on SARS-CoV-2 Spike Protein Based on Large-Scale Correlated Fragment Molecular Orbital Calculations

Kazuki Akisawa, Ryo Hatada, Koji Okuwaki, Yuji Mochizuki, Kaori Fukuzawa, Yuto Komeiji, Shigenori Tanaka

Version 1 posted 11 September 2020

850

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Theoretical and Computational Chemistry

Working Paper

Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease - Inhibitor N3 Complex (PDB ID:6LU7)

Ryo Hatada, Koji Okuwaki, Yuji Mochizuki, Kaori Fukuzawa, Yuto Komeiji, Yoshio Okiyama, Shigenori Tanaka

Version 1 posted 17 March 2020

2,090

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Physical Chemistry

Working Paper

Prediction of Binding Pose and Affinity of SARS-CoV-2 Main Protease and Repositioned Drugs by Combining Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations

Yuma Handa, Koji Okuwaki, Yusuke Kawashima, Ryo Hatada, Yuji Mochizuki, Yuto Komeiji, Shigenori Tanaka, Takayuki Furuishi, Etsuo Yonemochi, Teruki Honma, Kaori Fukuzawa

Version 1 posted 25 July 2023

213

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Physical Chemistry

Working Paper

Geometry Optimization using the Frozen Domain and Partial Dimer Approach with the Fragment Molecular Orbital Method: Implementation, Benchmark, and Application for Ligand-Binding Site of Proteins

Koji Okuwaki, Naoki Watanabe, Koichiro Kato, Chiduru Watanabe, Naofumi Nakayama, Akifumi Kato, Yuji Mochizuki, Tatsuya Nakano, Teruki Honma, Kaori Fukuzawa

Version 1 posted 24 July 2024

97

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Theoretical and Computational Chemistry

Working Paper

Towards Accurate Description of Chemical Reaction Energetics by Using Variational Quantum Eigensolver: A Case Study of the C2v Quasi-Reaction Pathway of Beryllium Insertion to H2 Molecule

Kenji Sugisaki, Takumi Kato, Yuichiro Minato, Koji Okuwaki, Yuji Mochizuki

Version 1 posted 25 June 2021

567

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8 results in Koji Okuwaki in Authors: Koji Okuwaki

Dynamical Cooperativity of Ligand-Residue Interactions Evaluated with the Fragment Molecular Orbital Method

Reduction of Orbital Space for Molecular Orbital Calculations with Quantum Computation Simulator for Educations

Fragment Molecular Orbital Based Interaction Analyses on Complexes Between RBD Variants and ACE2

Interaction Analyses on SARS-CoV-2 Spike Protein Based on Large-Scale Correlated Fragment Molecular Orbital Calculations

Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease - Inhibitor N3 Complex (PDB ID:6LU7)

Prediction of Binding Pose and Affinity of SARS-CoV-2 Main Protease and Repositioned Drugs by Combining Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations

Geometry Optimization using the Frozen Domain and Partial Dimer Approach with the Fragment Molecular Orbital Method: Implementation, Benchmark, and Application for Ligand-Binding Site of Proteins

Towards Accurate Description of Chemical Reaction Energetics by Using Variational Quantum Eigensolver: A Case Study of the C2v Quasi-Reaction Pathway of Beryllium Insertion to H2 Molecule

8 results in Authors: Koji Okuwaki