Kiyoshi Yagi

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 15

Top Venues

The journal of physical chemistry. B

Physical chemistry chemical physics : PCCP

Journal of chemical theory and computation

Nature communications

RIKEN

University of Tokyo (PHD)

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

Affiliation History

RIKEN Dec 01 2012

Japan

Senior Research Scientist :: Theoretical Molecular Science Laboratory, Cluster for Pioneering Research

Education History

University of Tokyo Apr 01 2001 - Mar 31 2004

Japan

PHD :: Applied Chemistry

Publications

Jaewoon Jung, Kiyoshi Yagi, Cheng Tan, Hiraku Oshima, Takaharu Mori, Isseki Yu, Yasuhiro Matsunaga, Chigusa Kobayashi, Shingo Ito, Diego Ugarte La Torre, Yuji Sugita
GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models. The journal of physical chemistry. B 128 (25) (2024)
Jaewoon Jung, Kiyoshi Yagi, Cheng Tan, Hiraku Oshima, Takaharu Mori, Isseki Yu, Yasuhiro Matsunaga, Chigusa Kobayashi, Shingo Ito, Diego Ugarte La Torre, Yuji Sugita
GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models. The journal of physical chemistry. B (2024)
Jaewoon Jung, Kiyoshi Yagi, Cheng Tan, Hiraku Oshima, Takaharu Mori, Isseki Yu, Yasuhiro Matsunaga, Chigusa Kobayashi, Shingo Ito, Diego Ugarte La Torre, Yuji Sugita
GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models. The journal of physical chemistry. B 128 (25) (2024)
Hiroki Otaki, Shun-Ichi Ishiuchi, Masaaki Fujii, Yuji Sugita, Kiyoshi Yagi
Similarity scores of vibrational spectra reveal the atomistic structure of pentapeptides in multiple basins. Physical chemistry chemical physics : PCCP (2024)
Hiroki Otaki, Shun-Ichi Ishiuchi, Masaaki Fujii, Yuji Sugita, Kiyoshi Yagi
Similarity scores of vibrational spectra reveal the atomistic structure of pentapeptides in multiple basins. Physical chemistry chemical physics : PCCP 26 (13) (2024)
Jaewoon Jung, Kiyoshi Yagi, Cheng Tan, Hiraku Oshima, Takaharu Mori, Isseki Yu, Yasuhiro Matsunaga, Chigusa Kobayashi, Shingo Ito, Diego Ugarte La Torre, Yuji Sugita
GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models. The journal of physical chemistry. B 128 (25) (2024)
Shingo Ito, Kiyoshi Yagi, Yuji Sugita
Allosteric regulation of β-reaction stage I in tryptophan synthase upon the α-ligand binding. The Journal of chemical physics 158 (11) (2023)
Kenjiro Hanaoka, Shimpei Iwaki, Kiyoshi Yagi, Takuya Myochin, Takayuki Ikeno, Hisashi Ohno, Eita Sasaki, Toru Komatsu, Tasuku Ueno, Motokazu Uchigashima, Takayasu Mikuni, Kazuki Tainaka, Shinya Tahara, Satoshi Takeuchi, Tahei Tahara, Masanobu Uchiyama, Tetsuo Nagano, Yasuteru Urano
General Design Strategy to Precisely Control the Emission of Fluorophores via a Twisted Intramolecular Charge Transfer (TICT) Process. Journal of the American Chemical Society 144 (43) (2022)
Shingo Ito, Kiyoshi Yagi, Yuji Sugita
Computational Analysis on the Allostery of Tryptophan Synthase: Relationship between α/β-Ligand Binding and Distal Domain Closure. The journal of physical chemistry. B 126 (17) (2022)
Kiyoshi Yagi, Yuji Sugita
Anharmonic Vibrational Calculations Based on Group-Localized Coordinates: Applications to Internal Water Molecules in Bacteriorhodopsin. Journal of chemical theory and computation 17 (8) (2021)
Jin-Feng Liu, Jinrong Yang, Xiao Cheng Zeng, Sotiris S Xantheas, Kiyoshi Yagi, Xiao He
Towards complete assignment of the infrared spectrum of the protonated water cluster H+(H2O)21. Nature communications 12 (1) (2021)
Kiyoshi Yagi, Shingo Ito, Yuji Sugita
Exploring the Minimum-Energy Pathways and Free-Energy Profiles of Enzymatic Reactions with QM/MM Calculations. The journal of physical chemistry. B 125 (18) (2021)
Kiyoshi Yagi, Kenta Yamada, Chigusa Kobayashi, Yuji Sugita
Anharmonic Vibrational Analysis of Biomolecules and Solvated Molecules Using Hybrid QM/MM Computations. Journal of chemical theory and computation 15 (3) (2019)
Bo Thomsen, Tomonori Kawakami, Isamu Shigemoto, Yuji Sugita, Kiyoshi Yagi
Weight-Averaged Anharmonic Vibrational Analysis of Hydration Structures of Polyamide 6. The journal of physical chemistry. B 121 (24) (2017)
Kiyoshi Yagi, Bo Thomsen
Infrared Spectra of Protonated Water Clusters, H+(H2O)4, in Eigen and Zundel Forms Studied by Vibrational Quasi-Degenerate Perturbation Theory. The journal of physical chemistry. A 121 (12) (2017)

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Publication Activity (10 Years)

Top Topics

Top Venues

Kiyoshi Yagi