Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics
Srivastava, Ashutosh, Nagai, Tetsuro, Srivastava, Arpita, Miyashita, Osamu, Tama, Florence
Published in International journal of molecular sciences (30.10.2018)
Published in International journal of molecular sciences (30.10.2018)
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Journal Article
Flexible fitting to cryo‐EM density map using ensemble molecular dynamics simulations
Miyashita, Osamu, Kobayashi, Chigusa, Mori, Takaharu, Sugita, Yuji, Tama, Florence
Published in Journal of computational chemistry (15.06.2017)
Published in Journal of computational chemistry (15.06.2017)
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Journal Article
Molecular size dependence on achievable resolution from XFEL single-particle 3D reconstruction
Nakano, Miki, Miyashita, Osamu, Tama, Florence
Published in Structural dynamics (Melville, N.Y.) (01.03.2023)
Published in Structural dynamics (Melville, N.Y.) (01.03.2023)
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Journal Article
Single‐particle XFEL 3D reconstruction of ribosome‐size particles based on Fourier slice matching: requirements to reach subnanometer resolution
Nakano, Miki, Miyashita, Osamu, Jonic, Slavica, Tokuhisa, Atsushi, Tama, Florence
Published in Journal of synchrotron radiation (01.07.2018)
Published in Journal of synchrotron radiation (01.07.2018)
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Journal Article
Conformational ensemble of an intrinsically flexible loop in mitochondrial import protein Tim21 studied by modeling and molecular dynamics simulations
Srivastava, Arpita, Bala, Siqin, Motomura, Hajime, Kohda, Daisuke, Tama, Florence, Miyashita, Osamu
Published in Biochimica et biophysica acta. General subjects (01.02.2020)
Published in Biochimica et biophysica acta. General subjects (01.02.2020)
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Journal Article
Computational Protocol for Assessing the Optimal Pixel Size to Improve the Accuracy of Single-particle Cryo-electron Microscopy Maps
Tiwari, Sandhya P, Chhabra, Sahil, Tama, Florence, Miyashita, Osamu
Published in Journal of chemical information and modeling (26.05.2020)
Published in Journal of chemical information and modeling (26.05.2020)
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Journal Article
Conformational Transitions of Adenylate Kinase: Switching by Cracking
Whitford, Paul C., Miyashita, Osamu, Levy, Yaakov, Onuchic, José N.
Published in Journal of molecular biology (09.03.2007)
Published in Journal of molecular biology (09.03.2007)
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Journal Article
High-resolution structure of phosphoketolase from Bifidobacterium longum determined by cryo-EM single-particle analysis
Nakata, Kunio, Miyazaki, Naoyuki, Yamaguchi, Hiroki, Hirose, Mika, Kashiwagi, Tatsuki, Kutumbarao, Nidamarthi H.V., Miyashita, Osamu, Tama, Florence, Miyano, Hiroshi, Mizukoshi, Toshimi, Iwasaki, Kenji
Published in Journal of structural biology (01.06.2022)
Published in Journal of structural biology (01.06.2022)
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Journal Article
Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory
Nakano, Miki, Tateishi-Karimata, Hisae, Tanaka, Shigenori, Tama, Florence, Miyashita, Osamu, Nakano, Shu-Ichi, Sugimoto, Naoki
Published in Nucleic acids research (02.12.2015)
Published in Nucleic acids research (02.12.2015)
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Journal Article
Crystal contact-free conformation of an intrinsically flexible loop in protein crystal: Tim21 as the case study
Bala, Siqin, Shinya, Shoko, Srivastava, Arpita, Ishikawa, Marie, Shimada, Atsushi, Kobayashi, Naohiro, Kojima, Chojiro, Tama, Florence, Miyashita, Osamu, Kohda, Daisuke
Published in Biochimica et biophysica acta. General subjects (01.02.2020)
Published in Biochimica et biophysica acta. General subjects (01.02.2020)
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Journal Article