KASAHARA Kota 笠原浩太

Researcher Number	90634965
Other IDs	https://orcid.org/0000-0003-0207-6271
Affiliation (based on the past Project Information) *help	2020 – 2022: 立命館大学, 生命科学部, 助教 2016 – 2018: 立命館大学, 生命科学部, 助教
Review Section/Research Field	Principal Investigator Basic Section 62010:Life, health and medical informatics-related / Biophysics Except Principal Investigator Basic Section 43020:Structural biochemistry-related / Biological Sciences
Keywords	Principal Investigator 分子シミュレーション / 分子動力学法 / 転写制御 / 転写因子 / 天然変性蛋白質 / 翻訳後修飾 / 天然変性領域 / 生体分子 / 計算物理 / 蛋白質 … More / 生物物理 / 蛋白質間相互作用 / 分子認識 / 分子間相互作用 / ペプチドデザイン / 統計力学 / 拡張アンサンブル / 構造バイオインフォマティクス / 蛍光相関法 / シミュレーション / たんぱく質デザイン … More Except Principal Investigator 全原子モデル / 膜蛋白質 / 効率的立体構造探索 / 阻害効果 / conformational selection / 自由エネルギー障壁 / orientation selection / fly-casting / 自由エネルギー地形 / 結合過程 / エンドセリンリセプター / ボセンタン / GPCR / ヌクレオソーム / ポリメラーゼ / 蛋白質 / 生体分子 / 生物物理 / 生体生命情報学 / 分子動力学計算 / 遺伝子 / 転写因子 Less

膜蛋白質 GPCR と薬剤化合物ボセンタンの結合自由エネルギー地形
- Principal Investigator
  
  肥後順一
- Project Period (FY)
  2021 – 2023
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Review Section
  
  Basic Section 43020:Structural biochemistry-related
- Research Institution
  Ritsumeikan University
Study of the phosphorylation latch mechanism for the transcriptional regulation via intrinsically disordered regionsPrincipal Investigator
- Principal Investigator
  
  笠原浩太
- Project Period (FY)
  2020 – 2021
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Review Section
  
  Basic Section 62010:Life, health and medical informatics-related
- Research Institution
  Ritsumeikan University
Computational design of novel proteins with weak interactionsPrincipal Investigator
- Principal Investigator
  
  Kasahara Kota
- Project Period (FY)
  2016 – 2018
- Research Category
  
  Grant-in-Aid for Young Scientists (B)
- Research Field
  
  Biophysics
- Research Institution
  Ritsumeikan University
Elucidation of information-processing mechanisms during transcription cycle using computational and information sciences
- Principal Investigator
  
  NAKAMURA Haruki
- Project Period (FY)
  2012 – 2016
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Biological Sciences
- Research Institution
  Osaka University

All 2022 2021 2020 2019 2018 2017 2016 2015 2014 2013 Other

All Journal Article Presentation Book

[Book] iｎｓｉｌｉｃｏ創薬におけるスクリーニングの高速化・高精度化技術2018
- Author(s)
  村上洋一、水口賢司、藤秀義、山岸賢司、坂本泰一、小沢知永、小澤基裕、石川吉伸、船津公人、廣明秀一、蟹江慧、伊藤圭祐、加藤竜司、上村みどり、栗田典之、佐藤裕徳、徳久淳師、金田亮、岩田浩明、笠原浩太、他
- Total Pages
  540
- Publisher
  技術情報協会
- ISBN
  4861046882
- Data Source
  KAKENHI-PROJECT-16K18526
[Journal Article] Fly-casting with ligand-sliding and orientational selection to support the complex formation of a GPCR and a middle-sized flexible molecule.2022
- Author(s)
  Junichi Higo, Kota Kasahara, et al.
- Journal Title
  
  BioRxiv
  
  Volume: -
- DOI
  10.1101/2022.02.28.482421
- Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06052
[Journal Article] Extended ensemble simulations of a SARS-CoV-2 nsp1-5'-UTR complex2022
- Author(s)
  *Shun Sakuraba, Qilin Xie, Kota Kasahara, Junichi Iwakiri, Hidetoshi Kono
- Journal Title
  
  PLoS Computational Biology
  
  Volume: 18 Issue: 1 Pages: 1-21
- DOI
  10.1371/journal.pcbi.1009804
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K12069, KAKENHI-PROJECT-20K12041
[Journal Article] Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles2022
- Author(s)
  Fukunishi Yoshifumi、Higo Junichi、Kasahara Kota
- Journal Title
  
  Biophysical Reviews
  
  Volume: 14 Issue: 6 Pages: 1423-1447
- DOI
  10.1007/s12551-022-01015-8
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-21K06052
[Journal Article] Fly casting with ligand sliding and orientational selection supporting complex formation of a GPCR and a middle sized flexible molecule.2022
- Author(s)
  Junichi Higo, Kota Kasahara, Gert-Jan Bekker, Benson Ma, Shun Sakuraba, Shinji Iida, Narutoshi Kamiya, Ikuo Fukuda, Hidetoshi Kono, Yoshifumi Fukunishi, Haruki Nakamura
- Journal Title
  
  Scientific Reports
  
  Volume: 12 Issue: 1 Pages: 13792-13792
- DOI
  10.1038/s41598-022-17920-7
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-21K06052, KAKENHI-PLANNED-18H05534
[Journal Article] Information quantity for secondary structure propensities of protein subsequences in the Protein Data Bank2022
- Author(s)
  Ryohei Kondo, *Kota Kasahara, Takuya Takahashi
- Journal Title
  
  Biophysics and Physicobiology
  
  Volume: 19 Issue: 0 Pages: n/a
- DOI
  10.2142/biophysico.bppb-v19.0002
- NAID
  130008162734
- ISSN
  2189-4779
- Language
  English
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K12069
[Journal Article] All-Atom Molecular Dynamics Elucidating Molecular Mechanisms of Single-Transmembrane Model Peptide Dimerization in a Lipid Bilayer2021
- Author(s)
  Itaya Hayato、Kasahara Kota、Xie Qilin、Yano Yoshiaki、Matsuzaki Katsumi、Takahashi Takuya
- Journal Title
  
  ACS Omega
  
  Volume: 6 Issue: 17 Pages: 11458-11465
- DOI
  10.1021/acsomega.1c00482
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K12069
[Journal Article] myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling2020
- Author(s)
  Kasahara Kota、Terazawa Hiroki、Itaya Hayato、Goto Satoshi、Nakamura Haruki、Takahashi Takuya、Higo Junichi
- Journal Title
  
  Biophysics and Physicobiology
  
  Volume: 17 Issue: 0 Pages: 140-146
- DOI
  10.2142/biophysico.BSJ-2020013
- NAID
  130007937194
- ISSN
  2189-4779
- Language
  English
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K12069
[Journal Article] GA-guided mD-VcMD: A genetic-algorithm-guided method for multi-dimensional virtual-system coupled molecular dynamics2020
- Author(s)
  Higo Junichi、Kusaka Ayumi、Kasahara Kota、Kamiya Narutoshi、Hayato Itaya、Qilin Xie、Takahashi Takuya、Fukuda Ikuo、Mori Kentaro、Hata Yutaka、Fukunishi Yoshifumi
- Journal Title
  
  Biophysics and Physicobiology
  
  Volume: 17 Issue: 0 Pages: 161-176
- DOI
  10.2142/biophysico.BSJ-2020008
- NAID
  130007977387
- ISSN
  2189-4779
- Language
  English
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K12069
[Journal Article] Multimodal Structural Distribution of the p53 C-Terminal Domain upon Binding to S100B via a Generalized Ensemble Method: From Disorder to Extradisorder2019
- Author(s)
  Iida Shinji、Kawabata Takeshi、Kasahara Kota、Nakamura Haruki、Higo Junichi
- Journal Title
  
  Journal of Chemical Theory and Computation
  
  Volume: 15 Issue: 4 Pages: 2597-2607
- DOI
  10.1021/acs.jctc.8b01042
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K05517, KAKENHI-PROJECT-17J07112, KAKENHI-PROJECT-16K18526
[Journal Article] Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi-modal interaction ensemble to an out-inhibitory state.2018
- Author(s)
  Kota Kasahara, Masaaki Shiina, Junichi Higo, Kazuhiro Ogata, Haruki Nakamura.
- Journal Title
  
  Nucleic Acids Research
  
  Volume: 46 Issue: 5 Pages: 2243-2251
- DOI
  10.1093/nar/gkx1297
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16K05517, KAKENHI-PROJECT-16K18526, KAKENHI-PROJECT-16K14711, KAKENHI-PROJECT-18K19305, KAKENHI-PROJECT-16H03293
[Journal Article] Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation2018
- Author(s)
  Kasahara Kota、Sakuraba Shun、Fukuda Ikuo
- Journal Title
  
  The Journal of Physical Chemistry B
  
  Volume: 122 Issue: 9 Pages: 2495-2503
- DOI
  10.1021/acs.jpcb.7b10830
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17K05143, KAKENHI-PROJECT-16K17778, KAKENHI-PROJECT-16K18526
[Journal Article] Molecular dynamics coupled with a virtual system for effective conformational sampling.2018
- Author(s)
  Tomonori Hayami, Kota Kasahara, Haruki Nakamura, Junichi Higo
- Journal Title
  
  J Comput Chem
  
  Volume: 1 Issue: 19 Pages: 1-1
- DOI
  10.1002/jcc.25196
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16K05517, KAKENHI-PROJECT-16K18526
[Journal Article] Unfolding of α-helical 20-residue poly-glutamic acid analyzed by multiple runs of canonical molecular dynamics simulations2018
- Author(s)
  Ogasawara Naoki、Kasahara Kota、Iwai Ryosuke、Takahashi Takuya
- Journal Title
  
  PeerJ
  
  Volume: 6 Pages: e4769-e4769
- DOI
  10.7717/peerj.4769
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16K18526
[Journal Article] Characteristics of interactions at protein segments without non-local intramolecular contacts in the Protein Data Bank2018
- Author(s)
  Kota Kasahara, Shintaro Minami, Yasunori Aizawa
- Journal Title
  
  PLoS One
  
  Volume: 13 Issue: 12 Pages: e0205052-e0205052
- DOI
  10.1371/journal.pone.0205052
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-17J02339, KAKENHI-PROJECT-16K18526
[Journal Article] Influence of various parameters in the replica-exchange molecular dynamics method: Number of replicas, replica-exchange frequency, and thermostat coupling time constant2018
- Author(s)
  Iwai Ryosuke、Kasahara Kota、Takahashi Takuya
- Journal Title
  
  Biophysics and Physicobiology
  
  Volume: 15 Issue: 0 Pages: 165-172
- DOI
  10.2142/biophysico.15.0_165
- NAID
  130007431701
- ISSN
  2189-4779
- Language
  English
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16K18526
[Journal Article] OpenCL-Based Implementation of an FPGA Accelerator for Molecular Dynamics Simulation.2017
- Author(s)
  Hasitha Muthumala Waidyasooriya, Masanori Hariyama, Kota Kasahara
- Journal Title
  
  Information Engineering Express
  
  Volume: 3 Pages: 11-23
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16K18526
[Journal Article] Molecular mechanisms of cooperative binding of transcription factors Runx1-CBFβ-Ets1 on the TCRα gene enhancer2017
- Author(s)
  Kasahara K, Shiina M, Fukuda I, Ogata K, Nakamura H
- Journal Title
  
  PloS One
  
  Volume: 12 Issue: 2 Pages: e0172654-e0172654
- DOI
  10.1371/journal.pone.0172654
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-ORGANIZER-24118001, KAKENHI-PLANNED-24118005, KAKENHI-PLANNED-24118008, KAKENHI-PROJECT-26330331, KAKENHI-PROJECT-16K18526, KAKENHI-PROJECT-16K14711, KAKENHI-PROJECT-16H03293
[Journal Article] An FPGA Accelerator for Molecular Dynamics Simulation Using OpenCL2017
- Author(s)
  Hasitha Muthumala Waidyasooriya, Masanori Hariyama and Kota Kasahara
- Journal Title
  
  International Journal of Networked and Distributed Computing
  
  Volume: Vol.5, No.1 Issue: 1 Pages: 52-61
- DOI
  10.2991/ijndc.2017.5.1.6
- Peer Reviewed / Acknowledgement Compliant / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15K15958, KAKENHI-PROJECT-16K18526
[Journal Article] Multi-dimensional virtual system introduced to enhance canonical sampling.2017
- Author(s)
  Junichi Higo, Kota Kasahara, Haruki Nakamura.
- Journal Title
  
  J. Chem. Phys.
  
  Volume: 147 Issue: 13 Pages: 134102-134102
- DOI
  10.1063/1.4986129
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16K05517, KAKENHI-PROJECT-16K18526, KAKENHI-PROJECT-16K14711
[Journal Article] Enhancement of canonical sampling by virtual-state transitions2017
- Author(s)
  Junichi Higo, Kota Kasahara, Bhaskar Dasgupta, Haruki Nakamura
- Journal Title
  
  J. Chem. Phys.
  
  Volume: 146 Issue: 4 Pages: 44104-44104
- DOI
  10.1063/1.4974087
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-ORGANIZER-24118001, KAKENHI-PLANNED-24118008, KAKENHI-PROJECT-16K14711, KAKENHI-PROJECT-16K18526, KAKENHI-PROJECT-16K05517
[Journal Article] myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme2016
- Author(s)
  Kota Kasahara, Benson Ma, Kota Goto, Bhaskar Dasgupta, Junichi Higo, Ikuo Fukuda, Tadaaki Mashimo, Yutaka Akiyama, Haruki Nakamura
- Journal Title
  
  Biophysics and Physicobiology
  
  Volume: 13 Issue: 0 Pages: 209-216
- DOI
  10.2142/biophysico.13.0_209
- NAID
  130007041560
- ISSN
  2189-4779
- Language
  English
- Peer Reviewed / Acknowledgement Compliant / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-ORGANIZER-24118001, KAKENHI-PLANNED-24118008, KAKENHI-PROJECT-16K05517, KAKENHI-PROJECT-16K18526
[Journal Article] IBiSA_Tools: A Computational Toolkit for Ion-Binding State Analysis in Molecular Dynamics Trajectories of Ion Channels2016
- Author(s)
  Kota Kasahara and Kengo Kinoshita
- Journal Title
  
  Plos One
  
  Volume: 11 Issue: 12 Pages: e0167524-e0167524
- DOI
  10.1371/journal.pone.0167524
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-PROJECT-15H02773, KAKENHI-PROJECT-16K18526
[Journal Article] mDCC_tools: Characterizing Multi-modal Atomic Motions in Molecular Dynamics Trajectories2016
- Author(s)
  Kota Kasahara, Neetha Mohan, Ikuo Fukuda, Haruki Nakamura
- Journal Title
  
  Bioinformatics
  
  Volume: 32 Issue: 16 Pages: 2531-2533
- DOI
  10.1093/bioinformatics/btw129
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-ORGANIZER-24118001, KAKENHI-PLANNED-24118008
[Journal Article] Landscape of protein-small ligand binding modes2016
- Author(s)
  Kota Kasahara, Kengo Kinoshita
- Journal Title
  
  Protein Science
  
  Volume: 25 Issue: 9 Pages: 1659-1671
- DOI
  10.1002/pro.2971
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16K18526
[Journal Article] Virtual-system coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking2015
- Author(s)
  Higo J, Dasgupta B, Mashimo T, Kasahara K, Fukunishi Y, Nakamura H
- Journal Title
  
  Journal of Computational Chemistry
  
  Volume: 36 Issue: 20 Pages: 1489-1501
- DOI
  10.1002/jcc.23948
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-ORGANIZER-24118001, KAKENHI-PLANNED-24118008
[Journal Article] A Novel Approach of Dynamic Cross Correlation Analysis on Molecular Dynamics Simulations and its Application to Ets1 dimer–DNA Complex2014
- Author(s)
  Kota Kasahara, Ikuo Fukuda, Haruki Nakamura
- Journal Title
  
  PLoS One
  
  Volume: 9 (11) Issue: 11 Pages: e112419-e112419
- DOI
  10.1371/journal.pone.0112419
- NAID
  120005596267
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-ORGANIZER-24118001, KAKENHI-PLANNED-24118008, KAKENHI-PROJECT-25390156
[Presentation] 転写因子PC4 の天然変性領域とテグメントタンパク質VP16 の結合メカニズムの計算科学的検討 / Simulation study of binding mechanism between intrinsically disordered region of transcription factor PC4 and tegument protein VP162021
- Author(s)
  謝祺琳、中野雄太、酒井佑介、笠原浩太、肥後順一、高橋卓也
- Organizer
  第59回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] TGIF-1 天然変性領域のリン酸化による機能制御機構の解析 / Molecular mechanism of functional regulation of TGIF-1 by phosphorylation on its intrinsically disordered region2021
- Author(s)
  中野雄太、謝祺琳、酒井佑介、仙石徹、笠原浩太、肥後順一、高橋卓也
- Organizer
  第21回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] 蛋白質配列上の電荷分布が液-液相分離現象に及ぼす影響の検討2021
- Author(s)
  笠原浩太
- Organizer
  第８回HPCIシステム利用研究課題成果報告会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] Helix ペプチド周囲の水和水ダイナミクスの分子動力学的研究 / Molecular dynamics study of hydration dynamics around Helix peptides2021
- Author(s)
  延永慎吾、笠原浩太、高橋卓也
- Organizer
  第21回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] 液-液相分離のシミュレーションに向けた粗視化分子モデルパラメータの開発 / Development of coarse-grained molecular model parameters for simulations of liquid-liquid phase separation2021
- Author(s)
  沖川純也、笠原浩太、高橋卓也
- Organizer
  第21回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] 分子動力学シミュレーションによるタンパク質の水和ダイナミクスと構造の相関解析/ Analysis of relationship between the hydration dynamics and the structures of model proteins with MD simulations2021
- Author(s)
  高橋卓也、藤澤太公也、延永慎吾、伊納竜太郎、中村優似、坂本渓、笠原浩太
- Organizer
  第59回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] 分子動力学法による転写調節因子 MED26 と３種の天然変性蛋白質それぞれの認識メカニズムの検討 / Molecular dynamics study on the multiple binding modes of MED26 to recognize three different intrinsically disordered proteins2021
- Author(s)
  後藤聡志、笠原浩太、肥後順一、高橋秀尚、高橋卓也
- Organizer
  第21回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] Molecular dynamics simulation of phosphorylated and unmodified intrinsically disordered region of TGIF-1 with its homeodomain2021
- Author(s)
  中野雄太、謝祺琳、酒井佑介、笠原浩太、仙石徹、肥後順一、高橋卓也
- Organizer
  第59回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] In silicoおよびin vitro実験によるTim4受容体―カーボンナノチューブ結合様式の解明 / Computational and biological analyses of Tim4-carbon nanotubes interactions2021
- Author(s)
  謝祺琳、大森聡、笠原浩太、山口慎一朗、高橋卓也、木下賢吾、中山勝文
- Organizer
  第48回日本毒性学会学術年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] Virtual-system coupled canonical MD 法による転写因子 PC4 の天然変性領域における VP16 結合メカニズムの検討 / Elucidation of binding mechanism between intrinsically disordered region of PC4 and VP16 by using virtual-system coupled canonical MD2021
- Author(s)
  謝祺琳、中野雄太、酒井佑介、笠原浩太、肥後順一、中山勝文、高橋卓也
- Organizer
  第21回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] Protein Data Bank の構造情報に基づく蛋白質－ペプチド間相互作用の網羅的な解析 / Comprehensive analysis of protein-peptide interactions based on Protein Data Bank structural information2021
- Author(s)
  佐藤圭一朗、笠原浩太、高橋卓也
- Organizer
  第21回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] Secondary structure propensities of amino acid N-grams in the Protein Data Bank2021
- Author(s)
  Ryohei Kondo、Kota Kasahara、Takuya Takahashi
- Organizer
  第10回生命医薬情報学連合大会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] ヘリックス傾向の異なる9 種類のペプチド周囲における水和ダイナミクスの分子動力学的研究 / Molecular dynamics study of hydrated water dynamics around 9 peptides with different helix propensity2021
- Author(s)
  延永慎吾、高橋卓也、笠原浩太
- Organizer
  第59回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] 新規 RUNX1 阻害薬候補化合物の結合様式に関する分子動力学法による解析 / Analysis of binding mechanisms of novel RUNX1 inhibitor candidates by using molecular dynamics simulations2021
- Author(s)
  酒井佑介、中野雄太、謝祺琳、笠原浩太、濱田恵輔、肥後順一、緒方一博、高橋卓也
- Organizer
  第21回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] Verification of simulations using Virtual system coupled canonical molecular dynamics for the small protein inhibitor2021
- Author(s)
  酒井佑介、中野雄太、謝祺琳、笠原浩太、肥後順一、高橋卓也
- Organizer
  第59回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] Molecular dynamics study on multiple binding modes of MED26 to recognize intrinsically disordered proteins. / 分子動力学法によるMED26の天然変性蛋白質認識メカニズムの検討2021
- Author(s)
  後藤聡志、笠原浩太、高橋秀尚、肥後順一、高橋卓也
- Organizer
  第59回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] 蛋白質天然変性領域における電荷分布が液- 液相分離現象に及ぼす影響に関する理論的検討 Theoretical study for influences of charge distribution along a protein sequence on the liquid-liquid phase separation2021
- Author(s)
  笠原浩太、寺澤裕樹、沖川純也、今村比呂志、肥後順一、加藤稔、高橋卓也
- Organizer
  第21回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] Virtual-system coupled canonical molecular dynamics法の開発と応用2021
- Author(s)
  笠原浩太
- Organizer
  第1回生体分子シミュレーション・モデリング研究会
- Invited
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] 仮想系共役サンプリング法の開発と応用 / Development and Application of the virtual-system coupled canonical sampling method2021
- Author(s)
  笠原浩太、謝祺琳、酒井佑介、中野雄太、肥後順一、高橋卓也
- Organizer
  第59回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] PDBbind データベースを用いた教師あり機械学習による蛋白質- リガンド相互作用予測手法の開発 Protein-small ligand interaction prediction method by supervised machine learning based on PDBBind database2021
- Author(s)
  Yuhang Chen、佐藤圭一朗、笠原浩太、Yuxiang Huang、高橋卓也
- Organizer
  第21回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] ドッキング構造予測のリランキングに向けた蛋白質―ペプチド間相互作用の網羅的解析 / Comprehensive analysis of protein-peptide interactions for reranking of docking predictions2021
- Author(s)
  佐藤圭一朗、笠原浩太、高橋卓也
- Organizer
  第59回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] コレステロールが膜貫通ペプチドの_量体化に与える影響に関する分_動_学的解析2020
- Author(s)
  板_颯_、笠原浩太、_野義明、松崎勝_、_橋卓也
- Organizer
  第58回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] 分_動_学法を_いたポリグルタミン酸周囲の_和ダイナミクス解析2020
- Author(s)
  藤澤太公也、_橋卓也、笠原浩太
- Organizer
  第58回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] 異なる配列と構造のペプチド周囲の_和ダイナミクスをMDシミュレーションで明らかにする2020
- Author(s)
  _橋卓也、延永慎吾、莇拓也、芦_凌惟、藤澤太公也、笠原浩太
- Organizer
  第58回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] Comprehensive classification of Protein-peptide interactions in the Protein Data Bank by using the Gaussian mixture model2020
- Author(s)
  Keiichiro Sato, Kota Kasahara, Takuya Takahashi
- Organizer
  第20回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] MED26によるTAF7とEAF1認識における多様な結合様式に関する分_動_学研究2020
- Author(s)
  後藤聡志、笠原浩太、_橋秀尚、_橋卓也
- Organizer
  第58回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] 分子シミュレーションで探る細胞膜脂質組成と蛋白質機能の関連2020
- Author(s)
  笠原浩太、板谷颯人、高橋卓也
- Organizer
  日本植物学会第84回大会
- Invited
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] PC4天然変性領域のVP16結合の制御メカニズムの解明2020
- Author(s)
  謝祺琳、笠原浩太、中_勝_、_橋卓也
- Organizer
  第58回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] PC4の天然変性領域における転写活性制御メカニズムの解明2020
- Author(s)
  謝祺琳、笠原浩太、中山勝文、高橋卓也
- Organizer
  第70回日本薬学会関西支部大会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] 荷電性残基の分布がタンパク質の液-液相分離に与える影響の解明に向けた分_動_学シミュレーション2020
- Author(s)
  寺澤裕樹、沖川純也、笠原浩太、今村_呂志、加藤稔、_橋卓也
- Organizer
  第58回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] Protein Data Bankに基づくタンパク質-ペプチド結合予測のための相互作_パターンの網羅的な分類と分析2020
- Author(s)
  佐藤圭_朗、笠原浩太、高橋卓也
- Organizer
  第58回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] Influences of cholesterol on dimerization of transmembrane peptides with a GxxxG motif studied by molecular dynamics simulations2020
- Author(s)
  Hayato Itaya, Kota Kasahara, Yoshiaki Yano, Katsumi Matzusaki, Takuya Takahashi
- Organizer
  第20回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] Multi-canonical Molecular Dynamics Study the Fuzzy Complex Formation by the Transcription Factor MED262020
- Author(s)
  Satoshi Goto, Kota Kasahara, Takuya Takahashi
- Organizer
  第20回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] Molecular Dynamics Study on Functional Regulation of Transcription Factors by Phosphorylation on the Intrinsically Disordered Region2020
- Author(s)
  Kota Kasahara, Toru Sengoku, Junichi Higo, Takuya Takahashi, Kazuhiro Ogata, Haruki Nakamura
- Organizer
  第20回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] __集合ペプチドのオリゴマー形成に関する分_動_学的解析2020
- Author(s)
  笠原浩太、沖川純也、寺澤裕樹、謝祺琳、後藤聡志、板_颯_、中_勝_、_橋卓也
- Organizer
  第58回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] 蛋白質―ペプチド間相互作用の網羅的解析と結合予測への応用2020
- Author(s)
  Keiichiro Sato, Kota Kasahara, Takuya Takahashi
- Organizer
  第9回生命医薬情報学連合大会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] リン脂質とステロールが膜貫通ペプチドの二量体形成に与える影響に関する分子動力学的検討2020
- Author(s)
  板谷颯人、笠原浩太、矢野義昭、松崎勝巳、高橋卓也
- Organizer
  日本植物学会第84回大会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] Phosphorylation on an intrinsically disordered region regulates the DNA binding activity of a transcription factor via transient interactions.2020
- Author(s)
  Kota Kasahara, Toru Sengoku, Qilin Xie, Yuta Nakano, Ryotaro Koike, Satoshi Fukuchi, Junichi Higo, Masafumi Nakayama, Kazuhiro Ogata, Takuya Takahashi
- Organizer
  第9回生命医薬情報学連合大会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] Coarse-grained molecular dynamics simulations to dissect effects of charge distributions in protein sequences on liquid-liquid phase separation2020
- Author(s)
  Hiroki Terazawa, Kota Kasahara, Takuya Takahashi
- Organizer
  第20回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-20K12069
[Presentation] FREE ENERGY LANDSCAPE OF THE P53 C TERMINAL DOMAIN UPON BINDING TO S100B: FROM DISORDER TO EXTRADISORDER2019
- Author(s)
  Junichi Higo、Iida Shinji、Takeshi Kawabata、Kota Kasahara、Haruki Nakamura
- Organizer
  63th annual meeting of the biophysical society
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] 蛋白質天然変性領域と相分離現象の分子機構解明に向けた分子シミュレーション技術の開発2019
- Author(s)
  笠原浩太
- Organizer
  第2回LLPS研究会
- Invited
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] 分子シミュレーションで迫る蛋白質相互作用の fuzziness2019
- Author(s)
  笠原浩太
- Organizer
  第11回BKCバイオインフォマティクス研究会
- Invited
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Molecular dynamics study on high-dimensional free-energy landscape of amyloid peptide higher-order complexes アミロイドペプチド高次複合体形成に関する高次元自由エネルギー地形の分子動力学的解析2018
- Author(s)
  Kota Kasahara、Junichi Higo、Tomonori Hayami、Takuya Takahashi
- Organizer
  第56回日本生物物理学会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Molecular dynamics simulations of liquid droplet and aggregation formations of protein FUS タンパク質FUSの液滴・凝集形成に関する分子動力学シミュレーション2018
- Author(s)
  Hiroki Terasawa、Kota Kasahara、Takuya Takahashi
- Organizer
  第56回日本生物物理学会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Elucidation of the mechanism of protein-protein interaction between regions out of globular domains with molecular dynamics simulations. 分子動力学法を用いたタンパク質球状ドメイン外の相互作用メカニズムの解明2018
- Author(s)
  Takuya Shimato、Kota Kasahara、Junichi Higo、Takuya Takahashi
- Organizer
  第56回日本生物物理学会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] MD simulations and analysis of hydration dynamics around several types of solute molecules 各種溶質周囲の水分子ダイナミクスの分子動力学計算と解析2018
- Author(s)
  Takuya Takahashi、Kota Kasahara、Ryoi Ashida、Nobuya Hasegawa、Daigo Itsuji、Tomomi Kura
- Organizer
  第56回日本生物物理学会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Analysis of protein-protein interactions in region except for globular domain by using the molecular dynamics method / 球状ドメイン以外の領域でのタンパク質間相互作用に関する分子動力学的解析2018
- Author(s)
  Takuya Shimato、Ryohei Kondo、Kota Kasahara、Yasunori Aizawa、Junichi Higo、Takuya Takahashi
- Organizer
  第18回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] A new method to improve the accuracy for protein-small molecule docking by using interaction pattern fingerprint and machine learning. 相互作用パターンと機械学習を用いたタンパク質-低分子化合物ドッキング手法の改良2018
- Author(s)
  Fumiaki Sato、Kota Kasahara、Takuya Takahashi
- Organizer
  第56回日本生物物理学会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Predicting interactions between N-gram sequences in proteins by using Neural Network. ニューラルネットワークを用いたタンパク質N-gram配列間相互作用の予測2018
- Author(s)
  Ryohei Kondo、Kota Kasahara、Takuya Takahashi
- Organizer
  第56回日本生物物理学会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Phosphorylation of an intrinsically disordered region of Ets1 yields specific inhibitory interactions from multi-modal interactions / 転写因子Ets1 天然変性領域のリン酸化は特異的な相互作用形成によりDNA 結合を阻害する2018
- Author(s)
  Kota Kasahara、 Masaaki Shiina、 Junichi Higo、Kazuhiro Ogata、Haruki Nakamura
- Organizer
  第18回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] hp170025 独自の拡張アンサンブル法によるたんぱく質天然変性領域の機能解明2018
- Author(s)
  笠原浩太
- Organizer
  第5回「京」を中核とするHPCIシステム利用研究課題成果報告会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Molecular dynamics coupled with virtual system for effective conformational sampling2018
- Author(s)
  Tomonori Hayami、Takuya Shimato、Haruki Nakamura、Kota Kasahara、Junichi Higo
- Organizer
  第56回日本生物物理学会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] ペプチド高次複合体形成の高次元自由エネルギー地形に関する分子動力学的検討2018
- Author(s)
  笠原浩太
- Organizer
  蛋白研セミナー「生体分子内情報伝達機構の新展開」
- Invited
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Fast Processing of Biopolymer Structure Generation and Protein-Protein Interaction Analysis 生体高分子立体構造生成およびタンパク質間相互作用解析の高速処理について2018
- Author(s)
  Takanori Sugihara、Kota Kasahara、Junichi Higo、Ichio Shimada
- Organizer
  第56回日本生物物理学会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Influence of cholesterol on membrane protein complex formation by molecular dynamics simulations with model peptides モデルペプチドを用いたMDシミュレーションによる膜タンパク質複合体形成にコレステロールが及ぼす影響の検討2018
- Author(s)
  Hayato Itaya、Kota Kasahara、Katumi Matsuzaki、Yoshiaki Yano、Takuya Takahashi
- Organizer
  第56回日本生物物理学会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Prediction method for complex structures of protein and small molecule with Interaction Pattern Fingerprint and machine learning / 相互作用パターンフィンガープリントと機械学習によるタンパク質- リガンドドッキング2018
- Author(s)
  Fumiaki Sato、Kota Kasahara、Takuya Takahashi
- Organizer
  第18回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] N-gram analysis of amino acid sequences toward elucidating mechanisms of protein-protein interactions / タンパク質間相互作用メカニズムの解明に向けたアミノ酸N-gram 統計解析2018
- Author(s)
  Ryohei Kondo、Kota Kasahara、Takuya Takahashi
- Organizer
  第18回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] The dominant structure of polyglutamic acids under an acidic conditions analyzed by replica-exchange molecular dynamics simulations. / レプリカ交換分子動力学シミュレーションによる酸性条件下でのポリグルタミン酸の最安定構造2017
- Author(s)
  Ryosuke Iwai, Tetsuro Nagai, Kota Kasahara, Takuya Takahashi
- Organizer
  第55回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Clarification of molecular recognition for the intrinsically disordered region, p53 C-terminal domain / 天然変性領域であるp53C末端ドメインの、分子認識メカニズムの解明2017
- Author(s)
  Shinji Iida, Kota Kasahara, Haruki Nakamura, Junichi Higo
- Organizer
  蛋白質科学会第17回年会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Calculation of surface pH change of mitochondria due to aggregation / ミトコンドリア凝集に伴う表面ｐHの変化の計算2017
- Author(s)
  Takuya Takahashi, Kota Kasahara, Yoshihiro Ohta
- Organizer
  第55回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Molecular dynamics study on the relationship between the protein secondary structure and its hydration dynamics / 蛋白質の二次構造と水和ダイナミクスの相関に関する分子動力学的研究2017
- Author(s)
  Takafumi Fujiyoshi, Kota Kasahara, Takuya Takahashi
- Organizer
  第55回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Non-Ewald method for accurately and efficiently calculating electrostatic interactions in molecular simulations2017
- Author(s)
  Ikuo Fukuda, Narutoshi Kamiya, Kota Kasahara, Han Wang, Shun Sakuraba, Haruki Nakamura
- Organizer
  Conformational Ensembles from Experimental Data and Computer Simulations
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Structural variety of the linker connecting two DNA-binding subdomains of Oct4 / Oct4の2つのDNA結合サブドメインを結ぶlinker領域の構造多様性2017
- Author(s)
  Tomonori Hayami, Shoji Takada, Kota Kasahara, Haruki Nakamura, Junichi Higo
- Organizer
  蛋白質科学会第17回年会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Structural variety of the linker connecting two DNA-binding subdomains of Oct4 / Oct4の2つのDNA結合サブドメインを結ぶlinker領域の構造多様性2017
- Author(s)
  Tomonori Hayami, Shoji Takada, Kota Kasahara, Haruki Nakamura, Junichi Higo
- Organizer
  第55回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Virtual system coupled canonical molecular dynamics simulation to enhance sampling along a reaction coordinate2017
- Author(s)
  Bhaskar Dasgupta, Kota Kasahara, Haruki Nakamura, Junichi Higo
- Organizer
  第55回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Reproduction of the water mobility around an ion by introducing a new Lennard-Jones parameter. / イオン周囲の水分子の運動性を再現する新規Lennard-Jonesパラメータの検討2017
- Author(s)
  Yuki Takimoto, Kota Kasahara, Takuya Takahashi
- Organizer
  第55回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Multicanonical molecular dynamics study of transcription factor-DNA binding regulation via the intrinsically disordered region / マルチカノニカル分子動力学法を用いた転写因子天然変性領域によるDNA結合制御メカニズムの検討2017
- Author(s)
  Kota Kasahara, Masaaki Shiina, Junichi Higo, Kazuhiro Ogata, Takuya Takahashi, Haruki Nakamura
- Organizer
  第55回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Study on helix-coil transition stability of the termini of poly-glutamic acid using molecular dynamics method / ポリグルタミン酸のへリックスコイル転移における末端の安定性に関する分子動力学法による検討2017
- Author(s)
  Naoki Ogasawara, Ryosuke Iwai, Kota Kasahara, Takuya Takahashi
- Organizer
  第55回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Multi-modal Dynamic Cross Correlation (mDCC) 法の開発と転写因子-DNA複合体における動的相関ネットワークの解析2017
- Author(s)
  笠原浩太
- Organizer
  名古屋大学IGERセミナー
- Place of Presentation
  名古屋大学（愛知県名古屋市）
- Year and Date
  2017-02-28
- Invited
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] 天然変性領域による転写制御の分子機構2017
- Author(s)
  笠原浩太
- Organizer
  第５回関西４私大生命科学シンポジウム
- Place of Presentation
  関西学院会館光の間（兵庫県、西宮市）
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] たんぱく質-低分子リガンド分子間相互作用の大規模データベース解析2017
- Author(s)
  笠原浩太
- Organizer
  第５回関西４私大生命科学シンポジウム
- Place of Presentation
  関西学院大学（兵庫県西宮市）
- Year and Date
  2017-03-07
- Invited
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] 分子シミュレーションによる転写因子機能制御メカニズムの解明：天然変性、翻訳後修飾、協調的結合2017
- Author(s)
  笠原浩太
- Organizer
  第2回生物資源セミナー「構造生物学が拓く生命科学研究」
- Invited
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Statistical analysis of correlation between amino acid sequence and protein function based on using Protein Data Bank2017
- Author(s)
  Ryohei Kondo, Kota Kasahara, Takuya Takahashi
- Organizer
  第55回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Phosphorylation on intrinsic disordered region of Ets1 yields a specific interaction among many fuzzy interactions2017
- Author(s)
  Kota Kasahara, Masaaki Shiina, Junichi Higo, Kazuhiro Ogata, Haruki Nakamura
- Organizer
  The 5th APPA symposium
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Investigation of appropriate conditions for enhancing sampling efficiency of multi-canonical molecular dynamics. / 拡張アンサンブル分子動力学法のサンプリング効率向上のための最適条件の探索2017
- Author(s)
  Takuya Shimato, Kota Kasahara, Junichi Higo, Takuya Takahashi
- Organizer
  第55回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] A new prediction method for complex structures of protein and small molecule with machine learning. / 機械学習を用いたタンパク質と薬のドッキング予測2017
- Author(s)
  Fumiaki Sato, Kota Kasahara, Takuya Takahashi
- Organizer
  第55回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Multi-modal Dynamic Cross Correlation (mDCC) 法の開発と転写因子- DNA 複合体における動的相関ネットワークの解析2017
- Author(s)
  笠原浩太
- Organizer
  名古屋大学 IGER セミナー
- Place of Presentation
  名古屋大学（愛知県、名古屋市）
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] 天然変性領域による転写制御の分子機構2017
- Author(s)
  笠原浩太
- Organizer
  第５回関西４私大生命科学シンポジウム
- Place of Presentation
  関西学院大学（兵庫県西宮市）
- Year and Date
  2017-03-07
- Invited
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Landscape of Protein-Small ligand Binding Modes2016
- Author(s)
  笠原浩太
- Organizer
  第5回生命医薬情報学連合大会
- Place of Presentation
  東京国際交流館プラザ平成（東京都江東区）
- Year and Date
  2016-09-30
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] 天然変性領域の過渡的な相互作用による転写制御の分子機構2016
- Author(s)
  笠原浩太、椎名政昭、肥後順一、緒方一博、中村春木
- Organizer
  第16回日本蛋白質科学会年会
- Place of Presentation
  福岡国際会議場（福岡県、福岡市）
- Year and Date
  2016-06-07
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] Replica-exchange molecular dynamics study of pH dependent structural changes of polyglutamic acids, レプリカ交換分子動力学シミュレーションによる pHに依存したポリグルタミン酸の構造変化の研究2016
- Author(s)
  Ryosuke Iwai, Tetsuro Nagai, Kota Kasahara, Takuya Takahashi
- Organizer
  第54回日本生物物理学会年会
- Place of Presentation
  つくば国際会議場（茨城県つくば市）
- Year and Date
  2016-11-25
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] 計算・情報科学による転写サイクルにおける情報変換機構の解明2016
- Author(s)
  笠原浩太、Neetha Mohan、中村春木
- Organizer
  転写サイクル合同班会議2016
- Place of Presentation
  松島一の坊（宮城県宮城郡松島町）
- Year and Date
  2016-09-05
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] 零多重極子和法によるTrp-cage蛋白質のエネルギー地形解析2016
- Author(s)
  櫻庭俊、笠原浩太、福田育夫、池部仁善、原田隆平
- Organizer
  日本蛋白質科学会第16回年会
- Place of Presentation
  福岡国際会議場（福岡県福岡市）
- Year and Date
  2016-06-07
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] 分子シミュレーションにおける静電相互作用計算法：零多重極子法の理論と実際2016
- Author(s)
  福田育夫, Wang Han, 神谷成敏, 笠原浩太, 寺田透, 櫻庭俊, 中村春木
- Organizer
  第54回日本生物物理学会年会
- Place of Presentation
  つくば国際会議場（茨城県、つくば市）
- Year and Date
  2016-11-25
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] Effects of solvent pH and protein conformations on water dynamics around a denatured protein with molecular dynamics simulation / 分子動力学法を用いた蛋白質周囲の水和ダイナミクスの検討：溶媒条件と蛋白質構造の影響について2016
- Author(s)
  Takafumi Fujiyoshi, Naoki Ogasawara, Yuji Ezaki, Yuta Nonaka, Kota Kasahara, Takuya Takahashi
- Organizer
  第54回日本生物物理学会年会
- Place of Presentation
  つくば国際会議場（茨城県つくば市）
- Year and Date
  2016-11-26
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] 巨大生体分子の長時間 MD シミュレーションの開発と生体分子の構造機能相関の解明2016
- Author(s)
  鷹野優、Neetha Mohan、草鹿あゆみ、川端猛、笠原浩太、真下忠彰、神谷成敏、中村春木
- Organizer
  第８回「学際計算科学による新たな知の発展・統合・創出」シンポジウム
- Place of Presentation
  筑波大学計算科学研究センター（茨城県、つくば市）
- Year and Date
  2016-10-17
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] Insights Derived from Molecular Dynamics Simulations into the Subunit Assembly and Clamp Motions of Thermococcus kodakarensis RNA Polymerase2016
- Author(s)
  Neetha Mohan, Kota Kasahara, Akira Hirata, Haruki Nakamura
- Organizer
  第16回日本蛋白質科学会年会
- Place of Presentation
  福岡国際会議場（福岡県、福岡市）
- Year and Date
  2016-06-07
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] 天然変性領域の過渡的な相互作用による転写制御の分子機構2016
- Author(s)
  笠原浩太、椎名政昭、肥後順一、緒方一博、中村春木
- Organizer
  日本蛋白質科学会第16回年会
- Place of Presentation
  福岡国際会議場（福岡県福岡市）
- Year and Date
  2016-06-07
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Unfolding dynamics of poly-glutamic acid in using molecular dynamics method / 分子動力学法を用いた、ポリグルタミン酸のアンフォールドダイナミクス2016
- Author(s)
  Naoki Ogasawara, Ryosuke Iwai, Kota Kasahara Tetsuro Nagai, Takuya Takahashi
- Organizer
  第54回日本生物物理学会年会
- Place of Presentation
  つくば国際会議場（茨城県つくば市）
- Year and Date
  2016-11-26
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Development and Evaluations of a Fast and Accurate Non-Ewald Electrostatic Potential Scheme, the Zero-Multipole Summation Method 非エバルト静電ポテンシャル計算法” 零多重極子和法” の開発と検証2016
- Author(s)
  Kota Kasahara, Shun Sakuraba, Ikuo Fukuda, Jinzen Ikebe, Ryuhei Harada
- Organizer
  第54回日本生物物理学会年会
- Place of Presentation
  つくば国際会議場（茨城県つくば市）
- Year and Date
  2016-11-26
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] 分子シミュレーションで解き明かすK+チャネルにおけるイオン透過の微視的ダイナミクス Molecular Dynamics Study on Ion-conduction Mechanisms of a K+ channel2016
- Author(s)
  笠原浩太
- Organizer
  大阪大学蛋白質研究所セミナー "膜タンパク質の構造ダイナミクス"
- Place of Presentation
  大阪大学（大阪府吹田市）
- Year and Date
  2016-05-12
- Invited
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] Insights Derived from Molecular Dynamics Simulations into the Subunit Assembly and Clamp Motions of Thermococcus kodakarensis RNA Polymerase2016
- Author(s)
  Neetha Mohan, Kota Kasahara, Akira Hirata, Haruki Nakamura
- Organizer
  日本蛋白質科学会第16回年会
- Place of Presentation
  福岡国際会議場（福岡県福岡市）
- Year and Date
  2016-06-07
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] 巨大生体分子の長時間MDシミュレーションの開発と生体分子の構造機能相関の解明2016
- Author(s)
  鷹野優, Neetha Mohan, 草鹿あゆみ, 川端猛, 笠原浩太, 真下忠彰, 神谷成
- Organizer
  第８回「学際計算科学による新たな知の発展・統合・創出」シンポジウム
- Place of Presentation
  筑波大学（茨城県つくば市）
- Year and Date
  2016-10-18
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] 転写因子ディスオーダー領域の翻訳後修飾による機能制御機構の解明2016
- Author(s)
  笠原浩太, 肥後順一, 飯田慎仁, 速水智教
- Organizer
  第3回「京」を中核とするHPCIシステム利用研究課題成果報告会
- Place of Presentation
  コクヨホール（東京都品川区）
- Year and Date
  2016-10-21
- Invited
- Data Source
  KAKENHI-PROJECT-16K18526
[Presentation] 転写因子Ets1とパートナー転写因子の協調的結合によるDNA結合活性制御機構の計算科学的検討2015
- Author(s)
  笠原浩太, 福田育夫, 中村春木
- Organizer
  第15回日本蛋白質科学会年会
- Place of Presentation
  あわぎんホール（徳島市）
- Year and Date
  2015-06-24
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] 分子シミュレーションから解き明かす転写因子Ets1のDNA結合調節機構2015
- Author(s)
  笠原浩太、Neetha Mohan、肥後順一、福田育夫、中村春木
- Organizer
  転写サイクル合同班会議2015
- Place of Presentation
  ホテル暖香園（静岡県伊東市）
- Year and Date
  2015-08-03
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] Interaction of two subunits of D/L hetero dimer with catalytic subunits in archaeal RNA polymerase: Insights from MD simulations2015
- Author(s)
  Neetha Mohan, 笠原浩太、平田章、中村春木
- Organizer
  第53回日本生物物理学会年会
- Place of Presentation
  金沢大学角間キャンパス（金沢市）
- Year and Date
  2015-09-13
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] 転写因子Ets1の天然変性領域によるDNA認識調節メカニズムに関する計算化学的検討2015
- Author(s)
  笠原浩太
- Organizer
  第3回天然変性蛋白質計算科学セミナー
- Place of Presentation
  御殿場高原時之栖、御殿場市
- Year and Date
  2015-03-11
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] 分子シミュレーションにおける静電相互作用計算のための新規非エバルト法2015
- Author(s)
  福田育夫, 神谷成敏, Han Wang, 笠原浩太、中村春木
- Organizer
  第53回日本生物物理学会年会
- Place of Presentation
  金沢大学角間キャンパス（金沢市）
- Year and Date
  2015-09-13
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] 転写因子Ets1天然変性領域のリン酸化によるDNA認識阻害メカニズムの検討2015
- Author(s)
  笠原浩太、肥後順一、椎名政昭、緒方一博、中村春木
- Organizer
  第53回日本生物物理学会年会
- Place of Presentation
  金沢大学角間キャンパス（金沢市）
- Year and Date
  2015-09-13
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] 共用スパコンを用いた分子動力学シミュレーション研究2014
- Author(s)
  笠原浩太
- Organizer
  国立遺伝学研究所スーパーコンピュータユーザ会
- Place of Presentation
  国立遺伝学研究所、三島市
- Year and Date
  2014-07-22
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] Molecular dynamics study on cooperative binding of Ets1 and partner transcription factors on regulatory elements2014
- Author(s)
  Kota Kasahara, Ikuo Fukuda, Haruki Nakamura
- Organizer
  第52回日本生物物理学会年会
- Place of Presentation
  札幌コンベンションセンター
- Year and Date
  2014-09-25
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] 分子動力学法に基づいた新しい動的相関解析手法の開発と転写因子Ets-1-DNA結合機構解析への応用2014
- Author(s)
  笠原浩太、福田育夫、中村春木
- Organizer
  第14回日本蛋白質科学会年会
- Place of Presentation
  ワークピア横浜、横浜市
- Year and Date
  2014-06-25
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] Contact number diffusion model for the normal mode analysis of protein structure2014
- Author(s)
  Bhaskar Dasgupta, Kota Kasahara, Narutoshi Kamiya, Haruki Nakamura, Akira Kinjo
- Organizer
  第52回日本生物物理学会年会
- Place of Presentation
  札幌コンベンションセンター
- Year and Date
  2014-09-26
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] Molecular dynamics study on enhancer recognitions by cooperative binding of Ets1 and partner transcription factors2014
- Author(s)
  Kota Kasahara, Ikuo Fukuda, Haruki Nakamura
- Organizer
  The 4th Asia Pacific Protein Association (APPA 2014)
- Place of Presentation
  ICC Jeju, Korea
- Year and Date
  2014-05-18
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] Zero-dipole summation法を用いたエンハンソソーム制御メカニズムの分子動力学的解析2014
- Author(s)
  笠原浩太、福田育夫
- Organizer
  第1回「京」を中核とするHPCIシステム利用研究課題成果報告会
- Place of Presentation
  コクヨホール、東京品川
- Year and Date
  2014-10-31
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] GIANT: a web-server for analyzing protein–small ligand interactions based on statistically preferred patterns of atomic contacts2013
- Author(s)
  Kota Kasahara, Kengo Kinoshita
- Organizer
  ISMB/ECCB 2013
- Place of Presentation
  ICC Berlin, Berlin, Germany
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] Measuring similarity of binding modes between 3D structures of protein–small ligand complexes2013
- Author(s)
  笠原浩太
- Organizer
  JCUP IV
- Place of Presentation
  大手町サンスカイルーム（東京）
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] The zero-dipole summation method and its application to molecular simulation with homogenous and inhomogeneous systems2013
- Author(s)
  Ikuo Fukuda, Narutoshi Kamiya, Kota Kasahara, Haruki Nakamura
- Organizer
  The 12th Asia Pacific Physics Conference (APPC12)
- Place of Presentation
  幕張メッセ（千葉市）
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] Measuring similarity of binding modes between 3D structures of protein–small ligand complexes.
- Author(s)
  笠原浩太
- Organizer
  JCUP IV
- Place of Presentation
  大手町サンスカイルーム（東京）
- Year and Date
  2013-06-06 – 2013-06-07
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] 分子動力学シミュレーション解析のためのMulti-modal Dynamic Cross Correlation法の開発と応用
- Author(s)
  笠原浩太、福田育夫、中村春木
- Organizer
  第3回生命医薬情報学連合大会
- Place of Presentation
  仙台国際センター、仙台市
- Year and Date
  2014-10-02 – 2014-10-04
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] The zero-dipole summation method and its application to molecular simulation with homogenous and inhomogeneous systems
- Author(s)
  Ikuo Fukuda, Narutoshi Kamiya, Kota Kasahara, Haruki Nakamura
- Organizer
  The 12th Asia Pacific Physics Conference (APPC12)
- Place of Presentation
  幕張メッセ（千葉市）大手町サンスカイルーム（東京）
- Year and Date
  2013-07-15 – 2013-07-16
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] 分子動力学法を用いた転写因子アロステリック制御機構の検討
- Author(s)
  笠原浩太
- Organizer
  計算タンパク質科学研究会
- Place of Presentation
  鳴子観光ホテル（宮城県）
- Year and Date
  2013-09-18 – 2013-09-20
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] GIANT: a web- server for analyzing protein-small ligand interactions based on statistically preferred patterns of atomic contacts
- Author(s)
  Kota Kasahara, Kengo Kinoshita
- Organizer
  ISMB/ECCB 2013
- Place of Presentation
  ICC Berlin, Berlin, Germany
- Year and Date
  2013-07-18 – 2013-07-25
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] 転写因子Ets1のDNA結合制御に関する分子シミュレーション研究
- Author(s)
  笠原浩太，福田育夫，中村春木
- Organizer
  冬の若手ワークショップ 2014
- Place of Presentation
  舌切雀のお宿磯部ガーデン（軽井沢東磯部温泉）
- Year and Date
  2014-01-30 – 2014-02-01
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] GIANT: a database for pattern analysis of protein-small ligand atomic contacts
- Author(s)
  Kota Kasahara, Kengo Kinoshita
- Organizer
  第13回日本蛋白質科学会年会
- Place of Presentation
  とりぎん文化会館（鳥取市）
- Year and Date
  2013-06-12 – 2013-06-14
- Data Source
  KAKENHI-PLANNED-24118008
[Presentation] Molecular dynamics study on ion conduction mechanisms of a voltage-sensitive potassium channel
- Author(s)
  Kota Kasahara, Matsuyuki Shirota, Toshiyuki Saito, Hiroko Kondo, Kengo Kinoshita
- Organizer
  第51回日本生物物理学会年会
- Place of Presentation
  国立京都国際会館（京都市）
- Year and Date
  2013-10-28 – 2013-10-30
- Data Source
  KAKENHI-PLANNED-24118008

1. NAKAMURA Haruki (80134485)

# of Collaborated Projects: 1 results

# of Collaborated Products: 23 results
2. KAMIYA Narutoshi (80420462)

# of Collaborated Projects: 1 results

# of Collaborated Products: 6 results
3. KONO Hidetoshi (40291918)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
4. 藤井聡 (40452825)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
5. 皿井明倫 (20221286)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
6. 仙石徹 (60576312)

# of Collaborated Projects: 1 results

# of Collaborated Products: 4 results
7. 肥後順一 (80265719)

# of Collaborated Projects: 1 results

# of Collaborated Products: 7 results
8. Kamagata Kiyoto

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
9. Niwa Tatsuya

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
10. IIDA Midori

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
11. ISHI Shunsuke

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
12. 太田元規

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
13. 木下賢吾

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
14. 緒方一博

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
15. 福田育夫

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
16. Waidyasooriya Ha

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

KASAHARA Kota 笠原 浩太

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膜蛋白質 GPCR と薬剤化合物ボセンタンの結合自由エネルギー地形

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Study of the phosphorylation latch mechanism for the transcriptional regulation via intrinsically disordered regionsPrincipal Investigator

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Computational design of novel proteins with weak interactionsPrincipal Investigator

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Elucidation of information-processing mechanisms during transcription cycle using computational and information sciences

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[Book] 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

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[Journal Article] Fly-casting with ligand-sliding and orientational selection to support the complex formation of a GPCR and a middle-sized flexible molecule.2022

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[Journal Article] Extended ensemble simulations of a SARS-CoV-2 nsp1-5'-UTR complex2022

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[Journal Article] Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles2022

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[Journal Article] Fly casting with ligand sliding and orientational selection supporting complex formation of a GPCR and a middle sized flexible molecule.2022

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[Journal Article] Information quantity for secondary structure propensities of protein subsequences in the Protein Data Bank2022

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[Journal Article] All-Atom Molecular Dynamics Elucidating Molecular Mechanisms of Single-Transmembrane Model Peptide Dimerization in a Lipid Bilayer2021

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[Journal Article] myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling2020

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[Journal Article] GA-guided mD-VcMD: A genetic-algorithm-guided method for multi-dimensional virtual-system coupled molecular dynamics2020

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NAID

KASAHARA Kota 笠原浩太

[Book] iｎｓｉｌｉｃｏ創薬におけるスクリーニングの高速化・高精度化技術2018