Yasuhiro Matsunaga

ResearcherID Researcher Name Resolver ID ORCID

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 17

Top Topics

Molecular Dynamics Simulations

Machine Learning

Single Molecule

Top Venues

PLoS computational biology

The journal of physical chemistry. B

Antibodies (Basel, Switzerland)

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

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)
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)
Tomonori Ogane, Daisuke Noshiro, Toshio Ando, Atsuko Yamashita, Yuji Sugita, Yasuhiro Matsunaga
Development of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series images. PLoS computational biology 18 (12) (2022)
Tomonori Ogane, Daisuke Noshiro, Toshio Ando, Atsuko Yamashita, Yuji Sugita, Yasuhiro Matsunaga
Development of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series images. PLoS computational biology 18 (12) (2022)
Tomonori Ogane, Daisuke Noshiro, Toshio Ando, Atsuko Yamashita, Yuji Sugita, Yasuhiro Matsunaga
Development of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series images. PLoS computational biology 18 (12) (2022)
Tomonori Ogane, Daisuke Noshiro, Toshio Ando, Atsuko Yamashita, Yuji Sugita, Yasuhiro Matsunaga
Development of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series images. PLoS computational biology 18 (12) (2022)
Tomonori Ogane, Daisuke Noshiro, Toshio Ando, Atsuko Yamashita, Yuji Sugita, Yasuhiro Matsunaga
Development of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series images. PLoS computational biology 18 (12) (2022)
Taihei Murakami, Shigefumi Kumachi, Yasuhiro Matsunaga, Miwa Sato, Kanako Wakabayashi-Nakao, Hidekazu Masaki, Ryo Yonehara, Maiko Motohashi, Naoto Nemoto, Masayuki Tsuchiya
Construction of a Humanized Artificial VHH Library Reproducing Structural Features of Camelid VHHs for Therapeutics. Antibodies (Basel, Switzerland) 11 (1) (2022)
Tomonori Ogane, Daisuke Noshiro, Toshio Ando, Atsuko Yamashita, Yuji Sugita, Yasuhiro Matsunaga
Development of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series images. PLoS computational biology 18 (12) (2022)
Ren Higashida, Yasuhiro Matsunaga
Enhanced Conformational Sampling of Nanobody CDR H3 Loop by Generalized Replica-Exchange with Solute Tempering. Life (Basel, Switzerland) 11 (12) (2021)
Chigusa Kobayashi, Yasuhiro Matsunaga, Jaewoon Jung, Yuji Sugita
Structural and energetic analysis of metastable intermediate states in the E1P-E2P transition of Ca2+-ATPase. Proceedings of the National Academy of Sciences of the United States of America 118 (40) (2021)
Toru Niina, Yasuhiro Matsunaga, Shoji Takada
Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure. PLoS computational biology 17 (7) (2021)
Hiroshi Fujisaki, Kei Moritsugu, Yasuhiro Matsunaga
Exploring Configuration Space and Path Space of Biomolecules Using Enhanced Sampling Techniques-Searching for Mechanism and Kinetics of Biomolecular Functions. International journal of molecular sciences 19 (10) (2018)
Yasuhiro Matsunaga, Tsutomu Yamane, Tohru Terada, Kei Moritsugu, Hiroshi Fujisaki, Satoshi Murakami, Mitsunori Ikeguchi, Akinori Kidera
Energetics and conformational pathways of functional rotation in the multidrug transporter AcrB. eLife 7 (2018)
Yasuhiro Matsunaga, Yuji Sugita
Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning. eLife 7 (2018)