Results

謝辞の記載についてAcknowledgement remarks

雑誌論文Papers

1. Kenichiro Takaba, Duy Phuoc Tran, Akio Kitao
   Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins
   The Journal of Chemical Physics , 152 , 22 , 225101 (2020)
   DOI: 10.1063/5.0004654
   C01:2022  C01:2020   C01 Akio Kitao  
2. Hiroaki Hata, Duy Phuoc Tran, Mohamed Marzouk Sobeh, Akio Kitao
   Binding free energy of protein/ligand complexes calculated using dissociation Parallel Cascade Selection Molecular Dynamics and Markov state model
   Biophysics and physicobiology , 18 , 305-316 (2021)
   DOI: 10.2142/biophysico.bppb-v18.037
   C01:2022  C01:2020   C01 Akio Kitao  
3. Takeo Yamawaki, Misao Mizuno, Haruto Ishikawa, Kazuhiro Takemura, Akio Kitao, Yoshitsugu Shiro, Yasuhisa Mizutani
   Regulatory Switching by Concerted Motions on the Microsecond Time Scale of the Oxygen Sensor Protein FixL
   The Journal of Physical Chemistry B , 125 , 25 , 6847-6856 (2021)
   DOI: 10.1021/acs.jpcb.1c01885
   C01:2022  C01:2020   C01 Akio Kitao  
4. Steven Hayward, Akio Kitao
   The role of the half-turn in determining structures of Alzheimer’s Aβ wild-type and mutants
   Journal of Structural Biology , 213 , 4 , 107792 (2021)
   DOI: 10.1016/j.jsb.2021.107792
   C01:2022  C01:2020   C01 Akio Kitao  
5. Mohamed Marzouk Sobeh, Akio Kitao
   Dissociation Pathways of the p53 DNA Binding Domain from DNA and Critical Roles of Key Residues Elucidated by dPaCS-MD/MSM
   Journal of Chemical Information and Modeling , 62 , 5 , 1294–1307 (2022)
   DOI: 10.1021/acs.jcim.1c01508
   プレスリリース: https://www.titech.ac.jp/news/2022/063638
   C01:2022  C01:2020   C01 Akio Kitao  
6. Duy Phuoc Tran, Yuta Taira, Takumi Ogawa, Ryoga Misu, Yoshiki Miyazawa, Akio Kitao
   Inhibition of the hexamerization of SARS-CoV-2 endoribonuclease and modeling of RNA structures bound to the hexamer
   Sci. Rep. , 12 , 3860 (2022)
   DOI: doi.org/10.1038/s41598-022-07792-2
   プレスリリース: https://www.titech.ac.jp/news/2022/063494
   C01:2022  C01:2020   C01 Akio Kitao  
7. Satoshi Yamashita, Misao Mizuno, Kazuhiro Takemura, Akio Kitao, and Yasuhisa Mizutani
   Dependence of Vibrational Energy Transfer on Distance in a Four-Helix Bundle Protein: Equidistant Increments with the Periodicity of α Helices
   J. Phys. Chem. B , 126 , 17 , 3283–3290 (2022)
   DOI: 10.1021/acs.jpcb.2c00956
   C01:2022  C01:2020   C01 Akio Kitao  
8. Akio Kitao
   Principal Component Analysis and Related Methods for Investigating the Dynamics of Biological Macromolecules
   J , 5 , 2 , 298-317 (2022)
   DOI: 10.3390/j5020021
   C01:2022  C01:2020   C01 Akio Kitao  
9. J. Ono, U. Koshimizu, Y. Fukunishi, H. Nakai
   Multiple protonation states in ligand-free SARS-CoV-2 main protease revealed by large-scale quantum molecular dynamics simulations
   Chem. Phys. Lett. , 794 , 139489 (2022)
   DOI: 10.1016/j.cplett.2022.139489
   C01:2020   C01 Junichi Ono  
10. H. Nakai, T. Takemura, J. Ono, Y. Nishimura
    Quantum-Mechanical Molecular Dynamics Simulations on Secondary Proton Transfer in Bacteriorhodopsin using Realistic Models
    J. Phys. Chem. B , 125 , 39 , 10947–10963 (2021)
    DOI: 10.1021/acs.jpcb.1c06231
    C01:2020   C01 Junichi Ono  
11. Oda K, Nomura T, Nakane T, Yamashita K, Inoue K, Ito S, Vierock J, Hirata K, Maturana AD, Katayama K, Ikuta T, Ishigami I, Izume T, Umeda R, Eguma R, Oishi S, Kasuya G, Kato T, Kusakizako T, Shihoya W, Shimada H, Takatsuji T, Takemoto M, Taniguchi R, Tomita A, Nakamura R, Fukuda M, Miyauchi H, Lee Y, Nango E, Tanaka R, Tanaka T, Sugahara M, Kimura T, Shimamura T, Fujiwara T, Yamanaka Y, Owada S, Joti Y, Tono K, Ishitani R, Hayashi S, Kandori H, Hegemann P, Iwata S, Kubo M, Nishizawa T, Nureki O.
    Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin
    elife , 23 , e62389 (2021)
    DOI: 10.7554/eLife.62389
    プレスリリース: https://www.s.u-tokyo.ac.jp/ja/press/2021/7284/
    A01:  B01:  C01:  A01:2020  C01:2020   A01 So Iwata  A01 Tsukasa Kusakizako  B01 Eriko Nango  B01 Sigeki Owada  C01 Minoru Kubo  C01 Tetsunari Kimura  A01 Wataru Shihoya  A01 Kota Katayama  C01 Shigehiko Hayashi  
12. Ichiro Tanaka, Ryota Nishinomiya, Ryosuke Goto, Shun Shimazaki, Toshiyuki Chatake
    Recent Structural Insights on the Mechanism of Lysozyme Hydrolysis
    Acta Cryst. D , 77 , 288-292 (2021)
    DOI: 10.1107/S2059798321000346
    C01:2020   C01 Ichiro Tanaka  
13. J. Ono, M. Imai, Y. Nishimura, H. Nakai
    Hydroxide Ion Carrier for Proton Pumps in Bacteriorhodopsin: Primary Proton Transfer
    J. Phys. Chem. B , 124 , 39 , 8524–8539 (2020)
    DOI: 10.1021/acs.jpcb.0c05507
    C01:2020   C01 Junichi Ono  
14. Wolff, A. M., Young, I. D., Sierra, R. G., Brewster, A. S., Martynowycz, M. W., Nango, E., Sugahara, M., Nakane, T., Ito, K., Aquila, A., Bhowmick, A., Biel, J. T., Carbajo, S., Cohen, A. E., Cortez, S., Gonzalez, A., Hino, T., Im, D., Koralek, J. D., Kubo, M., Lazarou, T. S., Nomura, T., Owada, S., Samelson, A. J., Tanaka, T., Tanaka, R., Thompson, E. M., van den Bedem, H., Woldeyes, R. A., Yumoto, F., Zhao, W., Tono, K., Boutet, S., Iwata, S., Gonen, T., Sauter, N. K., Fraser, J. S., Thompson, M. C.
    Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals.
    IUCrJ , 7 , 2 , 306-323 (2020)
    DOI: https://doi.org/10.1107/S205225252000072X
    A01:  B01:  C01:  C01:2020   A01 So Iwata  B01 Eriko Nango  B01 Sigeki Owada  C01 Minoru Kubo  A01 Tomoya Hino  

書籍Books

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学会発表Presentations, Lectures

1. チャン フ ズイ, 畑　宏明,中矢　光, 北尾彰朗
   Benchmarking the free energy calculation of PaCS-MD/MSM
   第21回日本蛋白質科学会年会, ( 2021 , 6 )
   C01:2022  C01:2020   C01 Akio Kitao  
2. 平悠太、Duy Tran、北尾彰朗
   DNA binding mechanisms of the p53 C-terminal domain elucidated by MD simulation
   第58回日本生物物理学会年会, ( 2020 , 9 )
   C01:2022  C01:2020   C01 Akio Kitao  
3. Sobeh Mohamed Marzouk、北尾彰朗
   Investigating the dissociation process of DBD-p53/DNA complex by PaCS-MD and MSM
   第58回日本生物物理学会年会, ( 2020 , 9 )
   C01:2022  C01:2020   C01 Akio Kitao  
4. 宮澤佳希、Phuoc Duy Tran、竹村和浩、北尾彰朗
   PaCS-MD/MSM を用いたタンパク質複合体の速度定数評価(Kinetic rate evaluation for protein complexes by PaCS-MD/MSM)
   第58回日本生物物理学会年会, ( 2020 , 9 )
   C01:2022  C01:2020   C01 Akio Kitao  
5. 竹村和浩、北尾彰朗
   Unguided Binding MD of Protein-Protein Complexes by PPI-ColDock
   第58回日本生物物理学会年会, ( 2020 , 9 )
   C01:2022  C01:2020   C01 Akio Kitao  
6. 宮澤佳希、Duy Phuoc Tran、竹村和浩、北尾彰朗
   Protein-protein complex dissociation simulated by Parallel Cascade Selection Molecular Dynamics
   第20回日本蛋白質科学会年会, ( 2020 , 7 )
   C01:2022  C01:2020   C01 Akio Kitao  
7. Tran P. Duy、Akio Kitao
   Simulating the association/dissociation process of flexible protein complexes
   第20回日本蛋白質科学会年会, ( 2020 , 7 )
   C01:2022  C01:2020   C01 Akio Kitao  
8. 竹村和浩、北尾彰朗
   Unguided Binding MD of Protein-Protein Complexes by PPI-ColDock
   第20回日本蛋白質科学会年会, ( 2020 , 7 )
   C01:2022  C01:2020   C01 Akio Kitao  
9. Wijaya Tegar Nurwahyu、北尾彰朗
   Dynamics of Close-Open State of Candida antarctica Lipase B Obtained by Parallel Cascade Molecular Dynamics Simulation and The Markov State Model
   第10回日本生物物理学会関東支部会, ( 2021 , 3 )
   C01:2022  C01:2020   C01 Akio Kitao