Ryuhei Harada

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 42

Top Topics

Density Functional Theory

Binding Protein

Anterior Cruciate Ligament Reconstruction

Molecular Dynamics

Top Venues

Journal of chemical information and modeling

Journal of chemical theory and computation

Nature communications

Journal of computational chemistry

This page only lists publications with an associated author ORCID identifier.

Publications

Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Ribosome Tunnel Environment Drives the Formation of α-Helix during Cotranslational Folding. Journal of chemical information and modeling 64 (16) (2024)
Nalinee Kongkaew, Kowit Hengphasatporn, Yasuteru Shigeta, Thanyada Rungrotmongkol, Ryuhei Harada
Preferential Door for Ligand Binding and Unbinding Pathways in Inhibited Human Acetylcholinesterase. The journal of physical chemistry letters (2024)
Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Ribosome Tunnel Environment Drives the Formation of α-Helix during Cotranslational Folding. Journal of chemical information and modeling (2024)
Nalinee Kongkaew, Kowit Hengphasatporn, Yasuteru Shigeta, Thanyada Rungrotmongkol, Ryuhei Harada
Preferential Door for Ligand Binding and Unbinding Pathways in Inhibited Human Acetylcholinesterase. The journal of physical chemistry letters 15 (21) (2024)
Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Ribosome Tunnel Environment Drives the Formation of α-Helix during Cotranslational Folding. Journal of chemical information and modeling 64 (16) (2024)
Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Ribosome Tunnel Environment Drives the Formation of α-Helix during Cotranslational Folding. Journal of chemical information and modeling 64 (16) (2024)
Nalinee Kongkaew, Kowit Hengphasatporn, Yasuteru Shigeta, Thanyada Rungrotmongkol, Ryuhei Harada
Preferential Door for Ligand Binding and Unbinding Pathways in Inhibited Human Acetylcholinesterase. The journal of physical chemistry letters 15 (21) (2024)
Nalinee Kongkaew, Kowit Hengphasatporn, Yuwanda Injongkol, Pitchayathida Mee-Udorn, Liyi Shi, Panupong Mahalapbutr, Phornphimon Maitarad, Ryuhei Harada, Yasuteru Shigeta, Thanyada Rungrotmongkol, Alisa S Vangnai
Design of electron-donating group substituted 2-PAM analogs as antidotes for organophosphate insecticide poisoning. RSC advances 13 (46) (2023)
Yohei Munei, Kowit Hengphasatporn, Yuta Hori, Ryuhei Harada, Yasuteru Shigeta
Determination of the Association between Mesotrione Sensitivity and Conformational Change of 4-Hydroxyphenylpyruvate Dioxygenase via Free-Energy Analyses. Journal of agricultural and food chemistry (2023)
Ryuhei Harada, Rikuri Morita, Yasuteru Shigeta
Free-Energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods. Journal of chemical information and modeling 63 (1) (2022)
Yuya Nishida, Sachiko Yanagisawa, Rikuri Morita, Hideki Shigematsu, Kyoko Shinzawa-Itoh, Hitomi Yuki, Satoshi Ogasawara, Ken Shimuta, Takashi Iwamoto, Chisa Nakabayashi, Waka Matsumura, Hisakazu Kato, Chai Gopalasingam, Takemasa Nagao, Tasneem Qaqorh, Yusuke Takahashi, Satoru Yamazaki, Katsumasa Kamiya, Ryuhei Harada, Nobuhiro Mizuno, Hideyuki Takahashi, Yukihiro Akeda, Makoto Ohnishi, Yoshikazu Ishii, Takashi Kumasaka, Takeshi Murata, Kazumasa Muramoto, Takehiko Tosha, Yoshitsugu Shiro, Teruki Honma, Yasuteru Shigeta, Minoru Kubo, Seiji Takashima, Yasunori Shintani
Author Correction: Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases. Nature communications 13 (1) (2022)
Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Protein Structure Validation Derives a Smart Conformational Search in a Physically Relevant Configurational Subspace. Journal of chemical information and modeling (2022)
Yuya Nishida, Sachiko Yanagisawa, Rikuri Morita, Hideki Shigematsu, Kyoko Shinzawa-Itoh, Hitomi Yuki, Satoshi Ogasawara, Ken Shimuta, Takashi Iwamoto, Chisa Nakabayashi, Waka Matsumura, Hisakazu Kato, Chai Gopalasingam, Takemasa Nagao, Tasneem Qaqorh, Yusuke Takahashi, Satoru Yamazaki, Katsumasa Kamiya, Ryuhei Harada, Nobuhiro Mizuno, Hideyuki Takahashi, Yukihiro Akeda, Makoto Ohnishi, Yoshikazu Ishii, Takashi Kumasaka, Takeshi Murata, Kazumasa Muramoto, Takehiko Tosha, Yoshitsugu Shiro, Teruki Honma, Yasuteru Shigeta, Minoru Kubo, Seiji Takashima, Yasunori Shintani
Author Correction: Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases. Nature communications 13 (1) (2022)
Yuya Nishida, Sachiko Yanagisawa, Rikuri Morita, Hideki Shigematsu, Kyoko Shinzawa-Itoh, Hitomi Yuki, Satoshi Ogasawara, Ken Shimuta, Takashi Iwamoto, Chisa Nakabayashi, Waka Matsumura, Hisakazu Kato, Chai Gopalasingam, Takemasa Nagao, Tasneem Qaqorh, Yusuke Takahashi, Satoru Yamazaki, Katsumasa Kamiya, Ryuhei Harada, Nobuhiro Mizuno, Hideyuki Takahashi, Yukihiro Akeda, Makoto Ohnishi, Yoshikazu Ishii, Takashi Kumasaka, Takeshi Murata, Kazumasa Muramoto, Takehiko Tosha, Yoshitsugu Shiro, Teruki Honma, Yasuteru Shigeta, Minoru Kubo, Seiji Takashima, Yasunori Shintani
Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases. Nature communications 13 (1) (2022)
Hayato Aida, Yasuteru Shigeta, Ryuhei Harada
The role of ATP in solubilizing RNA-binding protein fused in sarcoma. Proteins 90 (8) (2022)
Ryuhei Harada, Rikuri Morita, Yasuteru Shigeta
Free-Energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods. Journal of chemical information and modeling 63 (1) (2022)
Ryuhei Harada, Rikuri Morita, Yasuteru Shigeta
Free-Energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods. Journal of chemical information and modeling (2022)
Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Structural Validation by the G -Factor Properly Regulates Boost Potentials Imposed in Conformational Sampling of Proteins. Journal of chemical information and modeling 62 (14) (2022)
Ryuhei Harada, Rikuri Morita, Yasuteru Shigeta
Free-Energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods. Journal of chemical information and modeling 63 (1) (2022)
Yuya Nishida, Sachiko Yanagisawa, Rikuri Morita, Hideki Shigematsu, Kyoko Shinzawa-Itoh, Hitomi Yuki, Satoshi Ogasawara, Ken Shimuta, Takashi Iwamoto, Chisa Nakabayashi, Waka Matsumura, Hisakazu Kato, Chai Gopalasingam, Takemasa Nagao, Tasneem Qaqorh, Yusuke Takahashi, Satoru Yamazaki, Katsumasa Kamiya, Ryuhei Harada, Nobuhiro Mizuno, Hideyuki Takahashi, Yukihiro Akeda, Makoto Ohnishi, Yoshikazu Ishii, Takashi Kumasaka, Takeshi Murata, Kazumasa Muramoto, Takehiko Tosha, Yoshitsugu Shiro, Teruki Honma, Yasuteru Shigeta, Minoru Kubo, Seiji Takashima, Yasunori Shintani
Author Correction: Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases. Nature communications 13 (1) (2022)
Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Structural Variations of Metallothionein with or without Zinc Ions Elucidated by All-Atom Molecular Dynamics Simulations. The journal of physical chemistry. B 125 (46) (2021)
Vladimir Sladek, Ryuhei Harada, Yasuteru Shigeta
Residue Folding Degree-Relationship to Secondary Structure Categories and Use as Collective Variable. International journal of molecular sciences 22 (23) (2021)
Hayato Aida, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
In silico mutational analyses reveal different ligand-binding abilities of double pockets of medaka fish taste receptor type 1 essential for efficient taste recognition. Physical chemistry chemical physics : PCCP 23 (36) (2021)
Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Independent Nontargeted Parallel Cascade Selection Molecular Dynamics (Ino-PaCS-MD) to Enhance the Conformational Sampling of Proteins. Journal of chemical theory and computation 17 (9) (2021)
Sho Ashida, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada
Phosphorylation in the accessory domain of yeast histone chaperone protein 1 exposes the nuclear export signal sequence. Proteins (2021)
Takunori Yasuda, Yasuteru Shigeta, Ryuhei Harada
Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis-Based Parallel Cascade Selection Molecular Dynamics. Journal of chemical information and modeling 60 (8) (2020)
Rikuri Morita, Kentaro Nakano, Yasuteru Shigeta, Ryuhei Harada
Molecular Mechanism for the Actin-Binding Domain of α-Actinin Ain1 Elucidated by Molecular Dynamics Simulations and Mutagenesis Experiments. The journal of physical chemistry. B 124 (39) (2020)
Vladimir Sladek, Ryuhei Harada, Yasuteru Shigeta
Protein Dynamics and the Folding Degree. Journal of chemical information and modeling 60 (3) (2020)
Ryuhei Harada, Kota Yamaguchi, Yasuteru Shigeta
Enhanced Conformational Sampling Method Based on Anomaly Detection Parallel Cascade Selection Molecular Dynamics: ad-PaCS-MD. Journal of chemical theory and computation 16 (10) (2020)
Ryuhei Harada, Vladimir Sladek, Yasuteru Shigeta
Nontargeted Parallel Cascade Selection Molecular Dynamics Based on a Nonredundant Selection Rule for Initial Structures Enhances Conformational Sampling of Proteins. Journal of chemical information and modeling 59 (12) (2019)
Ryuhei Harada, Ryunosuke Yoshino, Hiroaki Nishizawa, Yasuteru Shigeta
Temperature-pressure shuffling outlier flooding method enhances the conformational sampling of proteins. Journal of computational chemistry 40 (15) (2019)
Ryuhei Harada, Yasuteru Shigeta
Selection Rules for Outliers in Outlier Flooding Method Regulate Its Conformational Sampling Efficiency. Journal of chemical information and modeling 59 (9) (2019)
Ryuhei Harada, Vladimir Sladek, Yasuteru Shigeta
Nontargeted Parallel Cascade Selection Molecular Dynamics Using Time-Localized Prediction of Conformational Transitions in Protein Dynamics. Journal of chemical theory and computation 15 (9) (2019)
Ryuhei Harada, Yasuteru Shigeta
Hybrid Cascade-Type Molecular Dynamics with a Markov State Model for Efficient Free Energy Calculations. Journal of chemical theory and computation 15 (1) (2018)
Ryuhei Harada, Yasuteru Shigeta
Temperature-Shuffled Structural Dissimilarity Sampling Based on a Root-Mean-Square Deviation. Journal of chemical information and modeling 58 (7) (2018)
Ryuhei Harada, Yasuteru Shigeta
On-the-Fly Specifications of Reaction Coordinates in Parallel Cascade Selection Molecular Dynamics Accelerate Conformational Transitions of Proteins. Journal of chemical theory and computation 14 (6) (2018)
Ryuhei Harada, Yasuteru Shigeta
Temperature-shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteins. Journal of computational chemistry 38 (31) (2017)
Ryuhei Harada, Yu Takano, Yasuteru Shigeta
Common folding processes of mini-proteins: Partial formations of secondary structures initiate the immediate protein folding. Journal of computational chemistry 38 (11) (2017)
Ryuhei Harada, Yasuteru Shigeta
Self-Avoiding Conformational Sampling Based on Histories of Past Conformational Searches. Journal of chemical information and modeling 57 (12) (2017)
Ryuhei Harada, Yasuteru Shigeta
Structural dissimilarity sampling with dynamically self-guiding selection. Journal of computational chemistry 38 (22) (2017)
Yuzuru Ujiie, Wataru Tanaka, Kyohei Hanaoka, Ryuhei Harada, Megumi Kayanuma, Mitsuo Shoji, Takeshi Murakawa, Toyokazu Ishida, Yasuteru Shigeta, Hideyuki Hayashi
Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate Conformations. The journal of physical chemistry. B 121 (22) (2017)
Ryuhei Harada, Yasuteru Shigeta
Efficient Conformational Search Based on Structural Dissimilarity Sampling: Applications for Reproducing Structural Transitions of Proteins. Journal of chemical theory and computation 13 (3) (2017)