Kota KASAHARA 笠原浩太

Assistant Professor, Ritsumeikan Univ., Japan

Last update: 11 25, 2020

基本情報 Contact Information

氏名 Name
笠原 浩太 博士(科学) Kota KASAHARA, Ph.D.
職位 Position
助教 Assistant Professor
所属 Affiliation
立命館大学 生命科学部 生命情報学科 計算構造生物学研究室 Computational Structural Biology Lab., College of Life Sciences, Ritsumeikan University, Japan
住所 Address
525-8577 滋賀県草津市野路東1-1-1 立命館大学びわこ・くさつキャンパス バイオリンク4F 1-1-1, Noji-higashi, Kusatsu-shi, Shiga, 525-8577, Japan
ktkshr <at> fc.ritsumei.ac.jp

業績リスト Publication List

原著論文(査読付き) Articles

*: Corresponding author(s). / †: Joint first authors.

author title year journal issue pages doi pubmed url
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
*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
*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
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
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
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
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
*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
*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
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
*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
*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
*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
*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
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
*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
*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
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
*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
*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
*†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
†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
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
†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
*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
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
*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
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
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
†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
*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
*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
*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
Junichi Higo, Takeshi Kawabata, Ayumi Kusaka, Kota Kasahara, Narutoshi Kamiya, Ikuo Fukuda, Kentaro Mori, Yutaka Hata, Yoshifumi Fukunishi, Haruki Nakamura Molecular interaction mechanism of a 14-3-3 protein with a phosphorylated peptide elucidated by enhanced conformational sampling 2020 Journal of Chemical Information and Modeling 60(10) 4767-4880 doi: 10.1021/acs.jcim.0c00551 PubMed URL
Kota KasaharaKota Kasahara, Hiroki Terazawa, Hayato Itaya, Satoshi Goto, Haruki Nakamura, Takuya Takahashi, Junichi Higo myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling 2020 Biophysics and Physicobiology 17 140-146 doi: 10.2142/biophysico.BSJ-2020013 URL

日本語総説 Reviews (Japanese)

author title year journal issue pages doi url
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
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

書籍 Books (Japanese)

author title year publisher amazon
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
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
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
白木賢太郎編 "相分離生物学の全貌(現代化学増刊46)" 2020 東京化学同人 amazon

ソフトウェア/データベース Software/Database

Curriculum Vitae Curriculum Vitae

略歴 C.V.

1983年1月8日 Jan 8th, 1983
誕生 Hello, world.
1998年4月1日〜2003年3月19日 Apr 1st, 1998 − Mar 19th, 2003
国立長岡工業高等専門学校 物質工学科 Department of Material Engeneering, Nagaoka College, National Institute of Technology, Japan
2003年4月1日〜2005年3月27日 Apr 1st, 2003 − Mar 27, 2005
東北大学工学部 化学・バイオ系(宮本明教授) Department of Applied Chemistry, School of Engeneering, Tohoku University
Undergraduate student (Supervisor: Prof. Akira Miyamoto)
2005年4月1日〜2007年3月27日 Apr 1st, 2005 − Mar 27th, 2007
応用化学専攻 博士課程前期(宮本明教授)
Department of Applied Chemistry, Graduate School of Engeneering, Tohoku University
Master course student (Supervisor: Prof. Akira Miyamoto)
2007年4月1日〜2010年9月27日 Apr 1st, 2007 − Sep 27th, 2010
情報生命科学専攻 博士課程後期(高木利久教授)
Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo
Ph.D. course student (Supervisor: Prof. Toshihisa Takagi)
2008年4月〜2009年3月 Apr, 2008 − Mar, 2009
日本学術振興機構特別研究員(DC2) Research Fellow of the Japan Society for the Promotion of Science (DC2)
2010年10月1日〜2012年12月31日 Oct 1st, 2010 − Dec 31st, 2012
東北大学大学院情報科学研究科 応用情報科学専攻
Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University
Postdoc. (PI: Prof. Kengo Kinoshita)
2013年1月1日〜2016年3月31日 Jan 1st, 2013 − Mar 31st, 2016
大阪大学蛋白質研究所 附属蛋白質解析先端研究センター
Research Center for State-of-the-Art Functional Protein Analysis, Institute for Protein Research, Osaka University
Postdoc. (PI: Prof. Haruki Nakamura)
2016年4月1日〜現在 Apr 1st,2016 − Present
立命館大学 生命科学部 生命情報学科
Department of Bioinformatics, College of Life Sciences, Ritsumeikan University
Assistant Professor. (PI: Prof. Takuya Takahashi)

所属学会 Affiliated Academic Organizations

  • 日本蛋白質科学会 Protein Science Society of Japan
  • 日本生物物理学会 Biophisical Society of Japan
  • 日本バイオインフォマティクス学会 Japanese Society for Bioinformatics

受賞など Awards (Japanese)