Yasuhiro Matsunaga - Publications, H-index & Citations

Yasuhiro Matsunaga

Saitama University

20H指数

166论文数

1.6K被引数

收录论文 27

发表时间

Mechanistic Interpretability of Fine-Tuned Protein Language Models for Nanobody Thermostability Prediction 微调蛋白质语言模型在纳米抗体热稳定性预测中的机制可解释性

Bioinformatics

IF5.4

2026-09-19

OAAI

Taihei Murakami; Yuki Hashidate; Yasuhiro Matsunaga; null

AFM-Fold: Rapid Reconstruction of Protein Conformations from AFM Images AFM-Fold：基于AFM图像的快速蛋白质构象重建

Biophysical Journal

IF3.1

2026-06-19

OAAI

Tsuyoshi Kawai; Yasuhiro Matsunaga

Explicit description of viral capsid subunit shapes by unfolding dihedrons

COMMUNICATIONS BIOLOGY

IF5.1

2024-11-14

OAAI

Toyooka, Ryuya; Nishimoto, Seri; Tendo, Tomoya; Horiyama, Takashi; Tachi, Tomohiro; Matsunaga, Yasuhiro

Representation of Protein Dynamics Disentangled by Time-Structure-Based Prior

JOURNAL OF CHEMICAL THEORY AND COMPUTATION

IF5.5

2023-12-27

OAAI

Ishizone, Tsuyoshi; Matsunaga, Yasuhiro; Fuchigami, Sotaro; Nakamura, Kazuyuki

End-to-end differentiable blind tip reconstruction for noisy atomic force microscopy images

SCIENTIFIC REPORTS

IF3.9

2023-01-04

OAAI

Matsunaga, Yasuhiro; Fuchigami, Sotaro; Ogane, Tomonori; Takada, Shoji

Construction of a Humanized Artificial VHH Library Reproducing Structural Features of Camelid VHHs for Therapeutics

ANTIBODIES

IF2.7

2022-01-30

OAAI

Murakami, Taihei; Kumachi, Shigefumi; Matsunaga, Yasuhiro; Sato, Miwa; Wakabayashi-Nakao, Kanako; Masaki, Hidekazu; Yonehara, Ryo; Motohashi, Maiko; Nemoto, Naoto; Tsuchiya, Masayuki

Enhanced Conformational Sampling of Nanobody CDR H3 Loop by Generalized Replica-Exchange with Solute Tempering

LIFE-BASEL

IF3.4

2021-12-18

OAAI

Higashida, Ren; Matsunaga, Yasuhiro

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

IF9.1

2021-09-30

OAAI

Kobayashi, Chigusa; Matsunaga, Yasuhiro; Jung, Jaewoon; Sugita, Yuji

Coarse-Grained Modeling of Multiple Pathways in Conformational Transitions of Multi-Domain Proteins

JOURNAL OF CHEMICAL INFORMATION AND MODELING

IF5.3

2021-05-06

OAAI

Shinobu, Ai; Kobayashi, Chigusa; Matsunaga, Yasuhiro; Sugita, Yuji

Use of single-molecule time-series data for refining conformational dynamics in molecular simulations

CURRENT OPINION IN STRUCTURAL BIOLOGY

IF7

2020-04-01

OAAI

Matsunaga, Yasuhiro; Sugita, Yuji

Conformational Fluctuations and Changes of Sr-Ca2+-ATPase on the E1/E2 Transition

BIOPHYSICAL JOURNAL

IF3.1

2019-02-01

OAAI

Kobayashi, Chigusa; Matsunaga, Yasuhiro; Jung, Jaewoon; Sugita, Yuji

Integrative Modeling of Protein Dynamics from Time-Series Data of Single-Molecule Experiments and Molecular Dynamics Simulations

BIOPHYSICAL JOURNAL

IF3.1

2019-02-01

OAAI

Matsunaga, Yasuhiro; Sugita, Yuji

Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning

ELIFE

IF0

2018-05-03

OAAI

Matsunaga, Yasuhiro; Sugita, Yuji

Refining Markov state models for conformational dynamics using ensemble-averaged data and time-series trajectories

JOURNAL OF CHEMICAL PHYSICS

IF3.1

2018-04-30

PREAI

Matsunaga, Y.; Sugita, Y.

Energetics and conformational pathways of functional rotation in the multidrug transporter AcrB

ELIFE

IF0

2018-03-06

OAAI

Matsunaga, Yasuhiro; Yamane, Tsutomu; Terada, Tohru; Moritsugu, Kei; Fujisaki, Hiroshi; Murakami, Satoshi; Ikeguchi, Mitsunori; Kidera, Akinori

Combining Weighted Ensemble Method and Lyapunov Weighted Dynamics: Application to Proteins

BIOPHYSICAL JOURNAL

IF3.1

2018-02-01

OAAI

Fujisaki, Hiroshi; Moritsugu, Kei; Matsunaga, Yasuhiro; Suetani, Hiromichi

Tumor invasion to the arteries feeding the gallbladder as a novel risk factor for cholecystitis after metallic stent placement in distal malignant biliary obstruction

DIGESTIVE ENDOSCOPY

IF4.7

2017-12-21

PREAI

Sogabe, Yuko; Kodama, Yuzo; Honjo, Hajime; Aoyama, Ikuo; Muramoto, Yuya; Koga, Eri; Yanaidani, Takafumi; Kawai, Munenori; Yoshikawa, Teppei; Matsumoto, Shimpei; Matsumoto, Astushi; Mori, Yoshiharu; Ono, Chikage; Nishida, Miyu; Nishida, Yoshihiro; Mikami, Takao; Matsunaga, Yasuhiro; Miyamoto, Yukiko; Kitami, Motoya; Nishikawa, Koji; Kondo, Masahiko; Miyake, Naoki; Kawanami, Chiharu; Seno, Hiroshi

GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms

JOURNAL OF COMPUTATIONAL CHEMISTRY

IF4.8

2017-07-18

151

OAAI

Kobayashi, Chigusa; Jung, Jaewoon; Matsunaga, Yasuhiro; Mori, Takaharu; Ando, Tadashi; Tamura, Koichi; Kamiya, Motoshi; Sugita, Yuji

Sequential data assimilation for single-molecule FRET photon-counting data

JOURNAL OF CHEMICAL PHYSICS

IF3.1

2015-06-05

PREAI