Contact Information

Name
Kota KASAHARA, Ph.D.
Position
Assistant Professor
Affiliation
Computational Structural Biology Lab., College of Life Sciences, Ritsumeikan University, Japan
Address
1-1-1, Noji-higashi, Kusatsu-shi, Shiga, 525-8577, Japan
E-mail
ktkshr <at> fc.ritsumeikan.ac.jp

Publication List

Articles

  • *: Corresponding author(s). / †: Joint first authors.
    1. *Masatake Sugita, Masataka Hamano, Kota Kasahara, Takeshi Kikuchi, Fumio Hirata,
      "New Protocol for Predicting the Ligand-Binding Site and Mode Based on the 3D-RISM/KH Theory",
      2020, Journal of Chemical Theory and Computation, 16(4): 2864–2876, doi: 10.1021/acs.jctc.9b01069 URL
    2. *Junichi Higo, Kota Kasahara, Mitsuhito Wada, Bhaskar Dasgupta, Narutoshi Kamiya, Tomonori Hayami, Ikuo Fukuda, Yoshifumi Fukunishi, *Haruki Nakamura,
      "Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: Fly-casting mechanism",
      2019, Protein Engineering, Design and Selection, 32(7): 297–308, doi: 10.1093/protein/gzz029 PubMed URL
    3. *Kota Kasahara, Yuki Takimoto, Ryoi Ashida, Takuya Takahashi,
      "Effects of ion–water Lennard-Jones potentials on the hydration dynamics around a monovalent atomic ion in molecular dynamics simulations.",
      2019, Molecular Simulation, 46(2): 83-91, doi: 10.1080/08927022.2019.1675883 URL
    4. †Takuya Shimato, *†Kota Kasahara, Junichi Higo, Takuya Takahashi,
      "Effects of number of parallel runs and frequency of bias-strength replacement in generalized ensemble molecular dynamics simulations.",
      2019, PeerJ Physical Chemistry, 1:e4: 1–20, doi: 10.7717/peerj-pchem.4 URL
    5. Yusuke Nomoto, Yukihiro Kubota, Yuto Ohnishi, Kota Kasahara, Aimi Tomita, Takehiro Oshime, Hiroki Yamashita, Muhamad Fahmi, *Masahiro Ito,
      "Gene Cascade Finder: A tool for identification of gene cascades and its application in Caenorhabditis elegans",
      2019, PLoS ONE, 14(9):e0215187: 1–16, doi: 10.1371/journal.pone.0215187 PubMed URL
    6. Tomonori Hayami, Junichi Higo, Haruki Nakamura, *Kota Kasahara,
      "Multidimensional virtual-system coupled canonical molecular dynamics to compute free-energy landscapes of peptide multimer assembly",
      2019, Journal of Computational Chemistry, 40(28): 2453-2463, doi: 10.1002/jcc.26020 PubMed URL
    7. *Kota Kasahara, Hiroki Terazawa, Takuya Takahashi, Junichi Higo,
      "Studies on molecular dynamics of intrinsically disordered proteins and their fuzzy complexes: A mini-review",
      2019, Computational and Structural Biotechnology Journal, 17: 712-720, doi: 10.1016/j.csbj.2019.06.009 PubMed URL
    8. Shinji Iida, Takeshi Kawabata, Kota Kasahara, Haruki Nakamura, *Junichi Higo,
      "Multimodal Structural Distribution of the p53 C-Terminal Domain upon Binding to S100B via a Generalized Ensemble Method: From Disorder to Extradisorder",
      2019, Journal of Chemical Theory and Computation, 15(4): 2597-2607, doi: 10.1021/acs.jctc.8b01042 PubMed URL
    9. *Kota Kasahara, Shintaro Minami, Yasunori Aizawa,
      "Characteristics of interactions at protein segments without non-local intramolecular contacts in the Protein Data Bank",
      2018, PLoS ONE, 13(12): e0205052.: 1-14, doi: 10.1371/journal.pone.0205052 PubMed URL
    10. †Ryosuke Iwai, *†Kota Kasahara, Takuya Takahashi,
      "Influence of various parameters in the replica-exchange molecular dynamics method: Number of replicas, replica-exchange frequency, and thermostat coupling time constant",
      2018, Biophysics and Physicobiology, 15: 165-172, doi: 10.2142/biophysico.15.0_165 PubMed URL
    11. Tomonori Hayami, Kota Kasahara, Haruki Nakamura, *Junichi Higo,
      "Molecular Dynamics Coupled with a Virtual System for Effective Conformational Sampling",
      2018, Journal of Computational Chemistry, 39(19): 1291-1299, doi: 10.1002/jcc.25196 PubMed URL
    12. †Naoki Ogasawara​, *†Kota Kasahara​​, Ryosuke Iwai, Takuya Takahashi,
      "Unfolding of α-helical 20-residue poly-glutamic acid analyzed by multiple runs of canonical molecular dynamics simulations",
      2018, PeerJ, 6:e4769: 1-17, doi: 10.7717/peerj.4769 PubMed URL
    13. *†Kota Kasahara, *†Masaaki Shiina, Junichi Higo, Kazuhiro Ogata, Haruki Nakamura,
      "Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi-modal interaction ensemble to an auto-inhibitory state.",
      2018, Nucleic Acids Research, 46(5): 2243-2251, doi: 10.1093/nar/gkx1297 PubMed URL
    14. *Kota Kasahara, Shun Sakuraba, Ikuo Fukuda,
      "Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation",
      2018, The Journal of Physical Chemistry B, 122(9): 2495-2503, doi: 10.1021/acs.jpcb.7b10830 PubMed URL
    15. *Junichi Higo, Kota Kasahara, Haruki Nakamura,
      "Multi-dimensional virtual system introduced to enhance canonical sampling.",
      2017, The Journal of Chemical Physics, 147: 134102: 1-13, doi: 10.1063/1.4986129 PubMed URL
    16. Hasitha Muthumala Waidyasooriya, Masanori Hariyama, Kota Kasahara,
      "OpenCL-Based Implementation of an FPGA Accelerator for Molecular Dynamics Simulation.",
      2017, Information Engineering Express, 3(2): 11-23, URL
    17. *Kota Kasahara, Masaaki Shiina, Ikuo Fukuda, Kazuhiro Ogata, Haruki Nakamura,
      "Molecular mechanisms of cooperative binding of transcription factors Runx1–CBFβ–Ets1 on the TCRα gene enhancer.",
      2017, PLoS ONE, 12(2): e0172654: 1-18, doi:10.1371/journal.pone.0172654 PubMed URL
    18. *Junichi Higo, Kota Kasahara, Bhaskar Dasgupta, Haruki Nakamura,
      "Enhancement of canonical sampling by virtual-state transitions",
      2017, The Journal of Chemical Physics, 146: 044104: 1-12, doi: 10.1063/1.4974087 PubMed URL
    19. Hasitha Muthumala Waidyasooriya, Masanori Hariyama, Kota Kasahara,
      "An FPGA Accelerator for Molecular Dynamics Simulation Using OpenCL",
      2017, International Journal of Networked and Distributed Computing, 5(1): 52-61, doi: 10.1109/ICIS.2016.7550743 URL
    20. *Kota Kasahara, Kengo Kinoshita,
      "IBiSA_tools: A Computational Toolkit for Ion-binding State Analysis in Molecular Dynamics Trajectories of Ion Channels ",
      2016, PLoS ONE, 11(12): e0167524: 1-9, doi: 10.1371/journal.pone.0167524 PubMed URL
    21. *Kota Kasahara, Benson Ma, Kota Goto, Bhaskar Dasgupta, Junichi Higo, Ikuo Fukuda, Tadaaki Mashimo, Yutaka Akiyama, Haruki Nakamura,
      "myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme",
      2016, Biophysics and Physicobiology, 13: 209-216, doi: 10.2142/biophysico.13.0_209 PubMed URL
    22. *Kota Kasahara, Kengo Kinoshita,
      "Landscape of protein-small ligand binding modes.",
      2016, Protein Science, 25(9): 1659-1671, doi: 10.1002/pro.2971 PubMed URL
    23. *Kota Kasahara, Neetha Mohan, Ikuo Fukuda, Haruki Nakamura,
      "mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories",
      2016, Bioinformatics, 32(16): 2531-2533, doi: 10.1093/bioinformatics/btw129 PubMed URL
    24. Kota Kasahara, Matsuyuki Shirota, *Kengo Kinoshita,
      "Ion Concentration- and Voltage-Dependent Push and Pull Mechanisms of Potassium Channel Ion Conduction",
      2016, PLoS ONE, 11:e0150716: 1-15, doi: 10.1371/journal.pone.0150716 PubMed URL
    25. *Junichi Higo, Bhaskar Dasgupta, Tadaaki Mashimo, Kota Kasahara, Yoshifumi Fukunishi, Haruki Nakamura,
      "Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking.",
      2015, Journal of Computational Chemistry, 36(20): 1489-1501, doi: 10.1002/jcc.23948 PubMed URL
    26. *Kota Kasahara, Ikuo Fukuda, Haruki Nakamura,
      "A Novel Approach of Dynamic Cross Correlation Analysis on Molecular Dynamics Simulations and Its Application to Ets1 Dimer-DNA Complex.",
      2014, PLoS ONE, 9(11):e112419: 1-13, doi: 10.1371/journal.pone.0112419 PubMed URL
    27. Bhaskar Dasgupta, Kota Kasahara, Narutoshi Kamiya, Haruki Nakamura, *Akira R Kinjo,
      "Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics",
      2014, PLoS ONE, 9:e91347: 1-16, do+I6i: 10.1371/journal.pone.0091347 PubMed URL
    28. Kota Kasahara, *Kengo Kinoshita,
      "GIANT: pattern analysis of molecular interactions in 3D structures of protein–small ligand complexes.",
      2014, BMC Bioinformatics, 15:12: 1-6, doi: 10.1186/1471-2105-15-12 PubMed URL
    29. Kota Kasahara, Matsuyuki Shirota, *Kengo Kinoshita,
      "Ion Concentration-Dependent Ion Conduction Mechanism of a Voltage-Sensitive Potassium Channel.",
      2013, PLoS ONE, 8:e56342: 1-8, doi: 10.1371/journal.pone.0056342 PubMed URL
    30. Kota Kasahara, Matsuyuki Shirota, *Kengo Kinoshita,
      "Comprehensive classification and diversity assessment of atomic contacts in protein-small ligand interactions.",
      2013, Journal of Chemical Information and Modeling, 53(1): 241-248, doi: 10.1021/ci300377f PubMed URL
    31. *Takeshi Obayashi, Kozo Nishida, Kota Kasahara, Kengo Kinoshita,
      "ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants.",
      2011, Plant and Cell Physiology, 52: 213-219, doi: 10.1093/pcp/pcq203 PubMed URL
    32. *Kota Kasahara, Kengo Kinoshita, Toshihisa Takagi,
      "Ligand-binding site prediction of proteins based on known fragment-fragment interactions.",
      2010, Bioinformatics, 26(12): 1493-1499, doi: 10.1093/bioinformatics/btq232 PubMed URL
    33. Kota Kasahara, Hideyuki Tsuboi, Michihisa Koyama, Akira Endou, Momoji Kubo, Calros Adriel Del Carpio, *Akira Miyamoto,
      "Tight-Binding Quantum Chemical Molecular Dynamics Study on First Proton Transfer Process of ORR Catalyzed by Cobalt-Porphyrin Complex.",
      2006, Electrochemical and Solid State Letters, 9: A490-A493, doi: 10.1149/1.2336985 URL

    Reviews (Japanese)

    1. 笠原浩太, 椎名政昭, 肥後順一, 緒方一博, 中村春木,
      "蛋白質の天然変性領域の化学修飾による特異的構造誘起と活性制御機構",
      2018, アンサンブル, 第20巻 第4号:253–259 URL
    2. 笠原浩太, 城田松之, 木下賢吾,
      "分子動力学シミュレーションによるタンパク質動的構造の解明:電位依存カリウムチャネルでの適用を例として",
      2013, 生化学, 第85巻 第8号:656–662 URL

    Books (Japanese)

    1. 技術情報協会編(笠原浩太他81名),
      "in silico創薬におけるスクリーニングの高速化・高精度化技術",
      2018, 技術情報協会, amazon
    2. 中村春木編(笠原浩太ほか9名),
      "見てわかる構造生命科学-生命科学研究へのタンパク質構造の利用",
      2014, 化学同人, amazon
    3. 柳田敏雄, 木下賢吾, 笠原浩太, 木寺詔紀 , 林重彦, 江口至洋, 高木周,
      "計算と生命(岩波講座 計算化学 第4巻)",
      2012, 岩波書店, amazon

    Software/Database

    Curriculum Vitae

    C.V.

    Jan 8th, 1983
    Hello, world.
    Apr,1st,1998−Mar,19th,2003
    Department of Material Engeneering, Nagaoka College, National Institute of Technology, Japan
    Apr,1st,2003−Mar,2005
    Department of Applied Chemistry, School of Engeneering, Tohoku University
    Undergraduate student
    (Supervisor: Prof. Akira Miyamoto)
    Apr,1st,2005−Mar,27th,2007
    Department of Applied Chemistry, Graduate School of Engeneering, Tohoku University
    Master course student
    (Supervisor: Prof. Akira Miyamoto)
    Apr,1st,2007−Sep,27th,2010
    Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo
    Ph.D. course student
    (Supervisor: Prof. Toshihisa Takagi)
    Apr,2008−Mar,2009
    Research Fellow of the Japan Society for the Promotion of Science (DC2)
    Oct,1st,2010−Dec,31st,2012
    Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University
    Postdoc.
    (PI: Prof. Kengo Kinoshita)
    Jan,1st,2013−Mar,31st,2016
    Research Center for State-of-the-Art Functional Protein Analysis, Institute for Protein Research, Osaka University
    Postdoc.
    (PI: Prof. Haruki Nakamura)
    Apr,1st,2016−Present
    Department of Bioinformatics, College of Life Sciences, Ritsumeikan University
    Assistant Professor.
    (PI: Prof. Takuya Takahashi)

    Affiliated Academic Organizations

    • Protein Science Society of Japan
    • Biophisical Society of Japan
    • Japanese Society for Bioinformatics