Terada Toru 寺田透

… Alternative Names

TERADA Tohru 寺田透

Less

Researcher Number	40359641
Other IDs
External Links
Affiliation (Current)	2025: 東京大学, 大学院農学生命科学研究科(農学部), 教授
Affiliation (based on the past Project Information) *help	2024 – 2025: 東京大学, 大学院農学生命科学研究科(農学部), 教授 2022 – 2024: 東京大学, 大学院農学生命科学研究科(農学部), 准教授 2016 – 2017: 東京大学, 大学院農学生命科学研究科(農学部), 特任准教授 2012 – 2015: 東京大学, 農学生命科学研究科, 准教授 2014: 東京大学, 大学院農学生命科学研究科, 准教授 … More 2012: 東京大学, 農学生命科学研究科, 特任准教授 2011: 東京大学, 大学院・農学生命科学研究科, 特任准教授 2007 – 2008: The University of Tokyo, Graduate School of Agricultural and Life Scienees, Project, Associate Professor 2005 – 2006: 東京大学, 大学院農学生命科学研究科, 特任助教授 2004 – 2005: 東京大学, 大学院・農学生命科学研究科, 特任助教授 2003: 東京大学, 大学院・農学生命科学研究科, 助手 Less
Review Section/Research Field	Principal Investigator Biophysics / Transformative Research Areas, Section (II) / Science and Engineering Except Principal Investigator Biological Sciences / Bioinformatics/Life informatics / Basic Section 43020:Structural biochemistry-related / Transformative Research Areas, Section (II) / Science and Engineering
Keywords	Principal Investigator 分子動力学シミュレーション / 粗視化モデル / パスウェイ / リガンド / タンパク質 / マルチカノニカル / 酵素・基質複合体 / AlphaFold / データベース / 触媒機構解析 … More / 機能予測 / 生合成関連酵素 / 触媒機構 / 複合体構造予測 / 立体構造予測 / 量子化学計算 / 変異体 / 粗視化分子動力学法 / リガンド結合シミュレーション / タンパク質－リガンド結合 / 最小自由エネルギー経路 / リガンド結合パスウェイ / transition path theory / マルコフ状態モデル / 自由エネルギープロファイル / マルチスケールシミュレーション / MARTINI / 自由エネルギー計算 / マルチコピー・マルチスケール法 / generalized Born / chignolin / Trp-cage / ミニ蛋白質 / 分子動力学 / フォールディング / Poisson方程式 / 一般化Bornモデル / クラスタ解析 / 立体構造変化 / calmodulin / 分子動力学法 … More Except Principal Investigator 構造予測 / 生体生命情報学 / プロテオーム / 蛋白質 / タンパク質 / 分子間相互作用 / 分子動力学法 / フラグメントアセンブリ方式 / ホモロジーモデリング / 植物 / 鉄錯体 / 膜タンパク質 / トランスポーター / 鉄 / 膜輸送体 / ムギネ酸 / クライオ電子顕微鏡 / 情報科学 / 計算科学 / 有機合成 / 生物合成 / 天然物化学 / 国際交流 / 天然有機化合物 / 生合成 / 反応機構 / 酵素 / 生物活性物質 / 生体分子 / molecular dynamics simulation / protein structure assessment / protein structure refinement / protein structure prediction / proteome / bioinformatics / 構造精密化 / 構造評価 / 分子動力学シミュレーション / 蛋白質構造評価 / 蛋白質構造精密化 / 蛋白質構造予測 / 予測機能 / 相互作用 / 糖 / バイオインフォマティクス / データベース / 相互作用予測 / 糖鎖 / 分子動力学 / 複合体 / 機能予測 / 資源管理 / ミドルウェア / グリッドコンピューティング / 分散共有メモリ / 並列計算 / ネットワーク / ソフトウェア学 / ハイパフォーマンス・コンピューティング / マルチカノニカル法 / アビニシオ法 / 構造クラスタリング / 統計ポテンシャル / ab initio法 Less

予知生合成科学・研究総括班
- Principal Investigator
  
  葛山智久
- Project Period (FY)
  2022 – 2026
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (A)
- Review Section
  
  Transformative Research Areas, Section (II)
- Research Institution
  The University of Tokyo
Development of a method to predict substrate and reaction specificities using predicted structuresPrincipal Investigator
- Principal Investigator
  
  寺田透
- Project Period (FY)
  2022 – 2026
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (A)
- Review Section
  
  Transformative Research Areas, Section (II)
- Research Institution
  The University of Tokyo
クライオ電顕を用いた鉄錯体輸送体の基質認識と輸送機構の解明
- Principal Investigator
  
  山形敦史
- Project Period (FY)
  2022 – 2024
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 43020:Structural biochemistry-related
- Research Institution
  Institute of Physical and Chemical Research
A theoretical verification of the ligand-binding-pathway hypothesisPrincipal Investigator
- Principal Investigator
  
  Terada Tohru
- Project Period (FY)
  2015 – 2017
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Research Field
  
  Biophysics
- Research Institution
  The University of Tokyo
Multi-scale simulation of protein-ligand binding processPrincipal Investigator
- Principal Investigator
  
  TERADA Tohru
- Project Period (FY)
  2012 – 2014
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Research Field
  
  Biophysics
- Research Institution
  The University of Tokyo
Development of protein-carbohydrate binding prediction systems and databases
- Principal Investigator
  
  SHIMIZU Kentaro
- Project Period (FY)
  2011 – 2014
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Research Field
  
  Bioinformatics/Life informatics
- Research Institution
  The University of Tokyo
ミニ蛋白質に共通するフォールディング機構の解明Principal Investigator
- Principal Investigator
  
  寺田透
- Project Period (FY)
  2007 – 2008
- Research Category
  
  Grant-in-Aid for Young Scientists (B)
- Research Field
  
  Biophysics
- Research Institution
  The University of Tokyo
高精度のドッキング機能を有するタンパク質間相互作用予測システムの開発
- Principal Investigator
  
  清水謙多郎
- Project Period (FY)
  2006 – 2007
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Review Section
  
  Biological Sciences
- Research Institution
  The University of Tokyo
高精度のドッキング機能を有するタンパク質間相互作用予測システムの開発
- Principal Investigator
  
  清水謙多郎
- Project Period (FY)
  2005
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Review Section
  
  Biological Sciences
- Research Institution
  The University of Tokyo
Development of methods for high-resolution protein structure modeling and for model structure assessment
- Principal Investigator
  
  SHIMIZU Kentaro
- Project Period (FY)
  2005 – 2007
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Research Field
  
  Bioinformatics/Life informatics
- Research Institution
  The University of Tokyo
ホモロジーモデリングとアビニシオ法の統合による高精度タンパク質構造予測手法の開発
- Principal Investigator
  
  清水謙多郎
- Project Period (FY)
  2004
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Review Section
  
  Biological Sciences
- Research Institution
  The University of Tokyo
大規模分散データの真に透過で効率的な共有を実現する分散共有配列システムの開発
- Principal Investigator
  
  清水謙多郎
- Project Period (FY)
  2004 – 2005
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Review Section
  
  Science and Engineering
- Research Institution
  The University of Tokyo
複合体形成に伴うタンパク質の立体構造変化パスウェイの予測・解析法の開発Principal Investigator
- Principal Investigator
  
  寺田透
- Project Period (FY)
  2004 – 2005
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Review Section
  
  Science and Engineering
- Research Institution
  The University of Tokyo
ホモロジーモデリングとアビニシオ法の統合による高精度タンパク質構造予測手法の開発
- Principal Investigator
  
  SHIMIZU Kentaro
- Project Period (FY)
  2003
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Review Section
  
  Biological Sciences
- Research Institution
  The University of Tokyo

All 2024 2023 2022 2017 2016 2015 2014 2013 2012 2008 2007 2006 2005 2004 Other

All Journal Article Presentation

[Journal Article] QM/MM Study of the Catalytic Mechanism and Substrate Specificity of the Aromatic Substrate C-Methyltransferase Fur62024
- Author(s)
  Zhao Fan、Moriwaki Yoshitaka、Noguchi Tomohiro、Shimizu Kentaro、Kuzuyama Tomohisa、Terada Tohru
- Journal Title
  
  Biochemistry
  
  Volume: 63 Issue: 6 Pages: 806-814
- DOI
  10.1021/acs.biochem.3c00556
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-21K12122, KAKENHI-PLANNED-22H05120, KAKENHI-PLANNED-22H05126
[Journal Article] Structural basis for the assembly and quinone transport mechanisms of the dimeric photosynthetic RC-LH1 supercomplex2022
- Author(s)
  Cao Peng、Bracun Laura、Yamagata Atsushi、Christianson Bern M.、Negami Tatsuki、Zou Baohua、Terada Tohru、Canniffe Daniel P.、Shirouzu Mikako、Li Mei、Liu Lu-Ning
- Journal Title
  
  Nature Communications
  
  Volume: 13 Issue: 1 Pages: 1977-1977
- DOI
  10.1038/s41467-022-29563-3
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-21H05733, KAKENHI-PROJECT-23K23828
[Journal Article] Uptake mechanism of iron-phytosiderophore from the soil based on the structure of yellow stripe transporter2022
- Author(s)
  Yamagata Atsushi、Murata Yoshiko、Namba Kosuke、Terada Tohru、Fukai Shuya、Shirouzu Mikako
- Journal Title
  
  Nature Communications
  
  Volume: 13 Issue: 1 Pages: 7180-7180
- DOI
  10.1038/s41467-022-34930-1
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-22K05342, KAKENHI-PROJECT-21K19051, KAKENHI-PUBLICLY-21H05733, KAKENHI-PROJECT-22H00352, KAKENHI-PROJECT-23K23828
[Journal Article] Overdominance effect of the bovine ghrelin receptor (GHSR1a)-DelR242 locus on growth in Japanese Shorthorn weaner bulls: Heterozygote advantage in bull selection and molecular mechanisms.2015
- Author(s)
  Masanori Komatsu, Yoichi Sato, Tatsuki Negami, Tohru Terada, Osamu Sasaki, Jumpei Yasuda, Aisaku Arakawa, Chikara Yoshida, Hideaki Takahashi, Aduli E.O. Malau-Aduli, Keiichi Suzuki and Kentaro Shimizu
- Journal Title
  
  G3: Genes, Genomes, Genetics
  
  Volume: Volume 5 Issue: 2 Pages: 271-279
- DOI
  10.1534/g3.114.016105
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-23300109
[Journal Article] Coarse-Grained Molecular Dynamics Simulations of Protein-Ligand Binding2014
- Author(s)
  Tatsuki Negami, Kentaro Shimizu, Tohru Terada
- Journal Title
  
  Journal of Computational Chemistry
  
  Volume: Volume 35 Issue: 25 Pages: 1835-1845
- DOI
  10.1002/jcc.23693
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-23300109, KAKENHI-PROJECT-24570179
[Journal Article] Structural Basis of the Divergent Oxygenation Reactions Catalyzed by the Rieske Nonheme Iron Oxygenase Carbazole 1,9a-Dioxygenase2014
- Author(s)
  Kengo Inoue, Yusuke Usami, Yuji Ashikawa, Haruko Noguchi, Takashi Umeda, Aiko Yamagami-Ashikawa, Tadafumi Horisaki, Hiromasa Uchimura, Tohru Terada, Shugo Nakamura, Kentaro Shimizu, Hiroshi Habe, Hisakazu Yamane, Zui Fujimoto and Hideaki Nojiri
- Journal Title
  
  Applied and Environmental Microbiology
  
  Volume: Volume 80 Issue: 9 Pages: 2821-2832
- DOI
  10.1128/aem.04000-13
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-23300109, KAKENHI-PROJECT-24780076, KAKENHI-PROJECT-26850052
[Journal Article] Heme binding mechanism of structurally similar iron-regulated surface determinant near transporter domains of Staphylococcus aureus exhibiting different affinities for heme.2013
- Author(s)
  Yoshitaka Moriwaki
- Journal Title
  
  Biochemistry
  
  Volume: 52 Issue: 49 Pages: 8866-8877
- DOI
  10.1021/bi4008325
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-13J06526, KAKENHI-PROJECT-23300109, KAKENHI-PROJECT-24000011, KAKENHI-PUBLICLY-24102516, KAKENHI-PROJECT-25249115, KAKENHI-PROJECT-25708026
[Journal Article] Selective binding of antimicrobial porphyrins to the hame-receptor IsdH-NEAT3 of Staphylococcus aureus.2013
- Author(s)
  Nhuan Vu
- Journal Title
  
  Protein Science
  
  Volume: 22 Issue: 7 Pages: 942-953
- DOI
  10.1002/pro.2276
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-13J06526, KAKENHI-PROJECT-23300109, KAKENHI-PROJECT-24000011, KAKENHI-PROJECT-25249115
[Journal Article] Understanding the roles of amino acid residues in tertiary structure formation of chignolin by using molecular dynamics simulation2008
- Author(s)
  T. Terada
- Journal Title
  
  PROTEINS: Structure, Function, and Bioinformatics, 掲載確定
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17500191
[Journal Article] A comparison of generalized Born methods in folding simulations2008
- Author(s)
  寺田透
- Journal Title
  
  Chemical Physics Letters 460
  
  Pages: 295-299
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19770126
[Journal Article] Understanding the roles of amino acid residues in tertiary structure formation of chignolin by using molecular dynamics simulation2008
- Author(s)
  寺田透
- Journal Title
  
  Proteins : Structure, Function, and Bioinformatics 73
  
  Pages: 621-631
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19770126
[Journal Article] Understanding the roles of amino acid residues in tertiary structure formation of chignolin by using molecular dynamics simulation2008
- Author(s)
  Tohru Terada
- Journal Title
  
  PROTEINS:Structure, Function, and Bioinformatics
- Description
  「研究成果報告書概要(和文)」より
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17500191
[Journal Article] Mechanism of the difference in the binding affinity of E.coli tRNAGln to glutaminyl-tRNA synthetase caused by non-interface nucleotides in variable loop2007
- Author(s)
  Satoshi Yamazaki, Shugo Nakamura, Tohru Terada, Kentaro Shimizu
- Journal Title
  
  Biophysical Journal 92
  
  Pages: 192-200
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-17500191
[Journal Article] A multicanonical ab initio molecular dynamics method : application to conformation sampling of alanine tripeptide2006
- Author(s)
  Ryota Jono, Tohru Terada, Kentaro Shimizu
- Journal Title
  
  Chemical Physics Letters 432
  
  Pages: 306-312
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-17500191
[Journal Article] Evaluation of efficiency of reference potential spatial warping algorithm in conformational sampling of peptides2006
- Author(s)
  Ryuichiro Ishitani, Tohru Terada, Kentaro Shimizu
- Journal Title
  
  Journal of Chemical Physics 124
  
  Pages: 214902-214902
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-17500191
[Journal Article] Insight of the Signal Motif of GPI-(like)-anchored Proteins by Using SVM2006
- Author(s)
  Wei Cao, Kazuya Sumikoshi, Tohru Terada, Shugo Nakamura, Kentaro Shimizu
- Journal Title
  
  Proceedings of the 2006 International Conference on Bioinformatics and Computational Biology(BIOCOMP'06)
  
  Pages: 541-546
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-17500191
[Journal Article] Folding free-energy landscape of a 10-residue mini-protein, chignolin2006
- Author(s)
  Daisuke Satoh, Tohru Terada, Shugo Nakamura, Kentaro Shimizu
- Journal Title
  
  FEBS Letters 580
  
  Pages: 3422-3426
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-17500191
[Journal Article] A fast protein-protein docking algorithm using series expansion in terms of spherical basis functions2005
- Author(s)
  Kazuya Sumikoshi, Tohru Terada, Shugo Nakamura, Kentaro Shimizu
- Journal Title
  
  Proceedings of the 16th International Conference on Genome Informatics(GIW2005) 16
  
  Pages: 161-173
- NAID
  130003997422
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-17500191
[Journal Article] マルチカノニカル分子動力学法によるリガンド結合に伴うタンパク質の構造変化メカニズムの解析2004
- Author(s)
  寺田透
- Journal Title
  
  生物物理 44,S1
- NAID
  110001157771
- Data Source
  KAKENHI-PROJECT-16014204
[Journal Article] Improvement of accuracy of free-energy landscapes of peptides calculated with generalized Born model by using numerical solutions of Poisson's equation.2004
- Author(s)
  Takanori Ishizuka, Tohru Terada, Shugo Nakamura, Kentaro Shimizu
- Journal Title
  
  Chemical Physics Letters 393
  
  Pages: 546-546
- Data Source
  KAKENHI-PROJECT-16041206
[Journal Article] Understanding the roles of amino acid residues in tertiary structure formation of chignolin by using molecular dynamics simulation
- Author(s)
  Tohru Terada, Daisuke Satoh, Tsutomu Mikawa, Yutaka Ito, Kentaro Shimizu
- Journal Title
  
  PROTEINS : Structure, Function, and Bioinformatics, accepted
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-17500191
[Journal Article] Refinement of comparative models of protein structure by using multicanonical molecular dynamics simulations
- Author(s)
  Ryuichiro Ishitani, Tohru Terada, Kentaro Shimizu
- Journal Title
  
  Molecular Simulation 34, 3
  
  Pages: 327-336
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-17500191
[Presentation] Predicting enzyme function using an empirical approach2023
- Author(s)
  Suguru Fujita, Tohru Terada
- Organizer
  日本生物物理学会第61回年会
- Data Source
  KAKENHI-PLANNED-22H05126
[Presentation] QM/MM study on the catalytic mechanism of the aromatic prenyltransferase Fur72023
- Author(s)
  Fan Zhao, Yoshitaka Moriwaki, Tomihisa Kuzuyama, Tohru Terada
- Organizer
  日本生物物理学会第61回年会
- Data Source
  KAKENHI-PLANNED-22H05126
[Presentation] Computational design of modified AzpC for peptide biosynthesis using nonnatural amino acids2023
- Author(s)
  Koki Miyake, Takashi Maruyama, Yoshitaka Moriwaki, Yohei Katsuyama, Yasuo Ohnishi, Tohru Terada
- Organizer
  日本生物物理学会第61回年会
- Data Source
  KAKENHI-PLANNED-22H05126
[Presentation] Computational analysis of the diazotization reaction mechanism of diazo-forming enzyme Fur52022
- Author(s)
  Shota Kaneko, Yoshitaka Moriwaki, Tomohiro Noguchi, Tomohisa Kuzuyama, Tohru Terada, Kentaro Shimizu
- Organizer
  日本生物物理学会第60回年会
- Data Source
  KAKENHI-PLANNED-22H05126
[Presentation] 分子動力学シミュレーションで探るタンパク質－リガンド相互作用2017
- Author(s)
  寺田　透
- Organizer
  2017年度生命科学系学会合同年次大会
- Invited
- Data Source
  KAKENHI-PROJECT-15K07021
[Presentation] A multiscale approach to understanding protein ligand binding process2016
- Author(s)
  Tohru Terada, Tatsuki Negami, Kentaro Shimizu
- Organizer
  Biophysical Society 60th Annual Meeting
- Place of Presentation
  Los Angeles Convention Center, Los Angeles, California, USA
- Year and Date
  2016-02-27
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15K07021
[Presentation] Protein-ligand interactions studied by molecular simulations2016
- Author(s)
  Tohru Terada, Yoshitaka Moriwaki, Tatsuki Negami, Kentaro Shimizu
- Organizer
  The 44th Symposium on Structure-Activity Relationship & the 31st Assembly for Pesticide Design Research
- Place of Presentation
  京都大学（京都府京都市）
- Year and Date
  2016-11-16
- Invited
- Data Source
  KAKENHI-PROJECT-15K07021
[Presentation] 分子シミュレーションで探るタンパク質－リガンド間相互作用2016
- Author(s)
  寺田　透、森脇由隆、根上　樹、吉野龍ノ介、清水謙多郎
- Organizer
  日本農芸化学会2016年度大会
- Place of Presentation
  札幌コンベンションセンター、札幌市
- Year and Date
  2016-03-27
- Invited
- Data Source
  KAKENHI-PROJECT-15K07021
[Presentation] Coarse-grained simulations of protein-ligand binding: effect of mutations near the ligand-binding pathways2016
- Author(s)
  Tatsuki Negami, Tohru Terada, Kentaro Shimizu
- Organizer
  日本生物物理学会第54回年会
- 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-15K07021
[Presentation] 粗視化分子動力学シミュレーションで探るタンパク質・リガンド結合過程2015
- Author(s)
  寺田　透
- Organizer
  CBI学会2015年大会
- Place of Presentation
  タワーホール船堀、東京都
- Year and Date
  2015-10-27
- Invited
- Data Source
  KAKENHI-PROJECT-15K07021
[Presentation] Protein-ligand binding pathways revealed by coarse-grained molecular dynamics simulations2015
- Author(s)
  Tatsuki Negami, Kentaro Shimizu, Tohru Terada
- Organizer
  CBI学会2015年大会
- Place of Presentation
  タワーホール船堀、東京都
- Year and Date
  2015-10-27
- Data Source
  KAKENHI-PROJECT-15K07021
[Presentation] A comparative study of the protein-ligand binding processes coupled to protein conformational change in coarse-grained simulation2015
- Author(s)
  Tatsuki Negami, Tohru Terada, Kentaro Shimizu
- Organizer
  日本生物物理学会第53回年会
- Place of Presentation
  金沢大学、金沢市
- Year and Date
  2015-09-13
- Data Source
  KAKENHI-PROJECT-15K07021
[Presentation] Structural insight into the heme-transfer mechanism between Isd proteins in Staphylococcus aureus2014
- Author(s)
  Yoshitaka Moriwaki, Tohru Terada, Jose M. M. Caaveiro, Kouhei Tsumoto, Kentaro Shimizu
- 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（北海道、札幌市）
- Year and Date
  2014-09-26
- Data Source
  KAKENHI-PROJECT-23300109
[Presentation] Protein-Ligand Binding Simulation with the Martini Coarse-Grained Force Field2014
- Author(s)
  Tatsuki Negami, Kentaro Shimizu, Tohru Terada
- Organizer
  Biophysical Society 58th Annual Meeting
- Place of Presentation
  Moscone Center, San Francisco, California, USA
- Data Source
  KAKENHI-PROJECT-24570179
[Presentation] PROTEIN-LIGAND BINDING SIMULATIONWITHTHE MARTINI COARSE-GRAINED FORCE FIELD.2014
- Author(s)
  Tatsuki Negami, Tohru Terada, Kentaro Shimizu
- Organizer
  Biophysical Society, 58th Annual Meeting
- Place of Presentation
  サンフランシスコ（アメリカ）
- Year and Date
  2014-02-18
- Data Source
  KAKENHI-PROJECT-23300109
[Presentation] HEME-TRANSFER MECHANISM OF STRUCTURALLY SIMILAR ISD NEAT DOMAINS OF STAPHYLOCOCCUS AUREUS EXHIBITING DIFFERENT AFFINITIES FOR HEME.2014
- Author(s)
  Yoshitaka Moriwaki, Tohru Terada, Jose M. M. Caaveiro, Yousuke Takaoka, Itaru Hamachi, Kouhei Tsumoto, Kentaro Shimizu
- Organizer
  Biophysical Society, 58th Annual Meeting
- Place of Presentation
  サンフランシスコ（アメリカ）
- Year and Date
  2014-02-19
- Data Source
  KAKENHI-PROJECT-23300109
[Presentation] タンパク質の複合体構造・相互作用に関する総合的な予測・解析/Prediction and analysis of protein complex structures and protein interactions2014
- Author(s)
  清水謙多郞、寺田透
- Organizer
  第14回日本蛋白質科学会年会
- Place of Presentation
  ワークピア横浜（神奈川県、横浜市）
- Year and Date
  2014-06-25
- Invited
- Data Source
  KAKENHI-PROJECT-23300109
[Presentation] The factors determining protein-ligand binding processes revealed by comparative coarse-grained simulations2014
- Author(s)
  Tatsuki Negami, Tohru Terada, Kentaro Shimizu
- 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（北海道、札幌市）
- Year and Date
  2014-09-26
- Data Source
  KAKENHI-PROJECT-23300109
[Presentation] 黄色ブドウ球菌のIsd-NEATドメイン間におけるヘム輸送についての考察2013
- Author(s)
  Yoshitaka Moriwaki, Tohru Terada, Jose M. M. Caaveiro, Yousuke Takaoka, Itaru Hamachi, Kouhei Tsumoto, Kentaro Shimizu
- Organizer
  日本生物物理学会　第51回年会
- Place of Presentation
  国立京都国際会館（京都府京都市）
- Year and Date
  2013-10-30
- Data Source
  KAKENHI-PROJECT-23300109
[Presentation] 代謝型グルタミン酸受容体の活性化過程の動的モデルの構築2013
- Author(s)
  冨士原　海太、根上　樹、寺田　透、清水　謙多郎
- Organizer
  日本生物物理学会　第51回年会
- Place of Presentation
  国立京都国際会館（京都府京都市）
- Year and Date
  2013-10-30
- Data Source
  KAKENHI-PROJECT-23300109
[Presentation] MARTINI粗視化力場を用いたタンパク質-リガンド結合過程の比較シュミレーション2013
- Author(s)
  根上樹、寺田　透、清水　謙多郎
- Organizer
  日本生物物理学会　第51回年会
- Place of Presentation
  国立京都国際会館（京都府京都市）
- Year and Date
  2013-10-29
- Data Source
  KAKENHI-PROJECT-23300109
[Presentation] 黄色ブドウ球菌のヘム輸送蛋白質群Isd system におけるその構造類似性とヘムの不可逆輸送に関する考察2013
- Author(s)
  Yoshitaka Moriwaki, Tohru Terada, Jose M. M. Caaveiro, Yousuke Takaoka, Itaru Hamachi, Kouhei Tsumoto, Kentaro Shimizu
- 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（鳥取県鳥取市）
- Year and Date
  2013-06-12
- Data Source
  KAKENHI-PROJECT-23300109
[Presentation] Comparative simulations of protein-ligand binding processes using the MARTINI coarse-grained force field2013
- Author(s)
  Tatsuki Negami, Tohru Terada, Kentaro Shimizu
- Organizer
  日本生物物理学会第51回年会
- Place of Presentation
  国立京都国際会館, 京都市
- Data Source
  KAKENHI-PROJECT-24570179
[Presentation] Coarse-grained MD simulations of ligand binding to proteins: Effect of the conformational changes of the proteins2012
- Author(s)
  Tatsuki Negami, Tohru Terada, Kentaro Shimizu
- Organizer
  日本生物物理学会第50回年会
- Place of Presentation
  名古屋大学（愛知県）
- Data Source
  KAKENHI-PROJECT-24570179
[Presentation] フォールディングシミュレーションにおけるgeneralized Bornモデルの比較2007
- Author(s)
  寺田透
- Organizer
  日本生物物理学会第45回年会
- Place of Presentation
  パシフィコ横浜
- Year and Date
  2007-12-22
- Data Source
  KAKENHI-PROJECT-19770126
[Presentation] Folding simulation of the B-domain of staphylococcal protein A2006
- Author(s)
  Ken-ichiro Nishi, Tohru Terada, Kentaro Shimizu
- Organizer
  Fifth East Asian Biophysics Symposium & Forty-Fourth Annual Meeting of the Biophysical Society of Japan, 46, 1P573
- Place of Presentation
  Okinawa
- Year and Date
  2006-11-13
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-17500191
[Presentation] Improving efficiency of conformation sampling in multicanonical molecular dynamics simulation2006
- Author(s)
  Tohru Terada, Kentaro Shimizu
- Organizer
  Fifth East Asian Biophysics Symposium & Forty-Fourth Annual Meeting of the Biophysical Society of Japan, 46, 1P581
- Place of Presentation
  Okinawa
- Year and Date
  2006-11-13
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-17500191
[Presentation] Improving efficiency of conformation sampling in multicanonical molecul ar dynamics simulation.2006
- Author(s)
  Tohru Terada
- Organizer
  Fifth East Asian Biophysics Symposium & Forty- Fourth Annual Meeting of the Biophysical Society of Japan
- Place of Presentation
  宜野湾
- Year and Date
  2006-11-13
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-17500191
[Presentation] Protein structure refinement by using multicanonical molecular dynamics simulation2005
- Author(s)
  Ryuichiro Ishitani, Tohru Terada, Shugo Nakamura, Kentaro Shimizu
- Organizer
  Forty-Third Annual Meeting of the Biophysical Society of Japan, 1P008
- Place of Presentation
  Sapporo
- Year and Date
  2005-11-23
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-17500191
[Presentation] The factors determining protein-ligand binding processes revealed by comparative coarse-grained simulations
- Author(s)
  Tatsuki Negami, Tohru Terada, Kentaro Shimizu
- Organizer
  日本生物物理学会第52回年会
- Place of Presentation
  札幌コンベンションセンター（北海道）
- Year and Date
  2014-09-25 – 2014-09-27
- Data Source
  KAKENHI-PROJECT-24570179
[Presentation] Protein-ligand binding processes studied by coarse-grained molecular dynamics simulations
- Author(s)
  Tohru Terada, Tatsuki Negami, Kentaro Shimizu
- Organizer
  日本生物物理学会第52回年会
- Place of Presentation
  札幌コンベンションセンター（北海道）
- Year and Date
  2014-09-25 – 2014-09-27
- Invited
- Data Source
  KAKENHI-PROJECT-24570179

1. SHIMIZU Kentaro (80178970)

# of Collaborated Projects: 7 results

# of Collaborated Products: 24 results
2. NAKAMURA Shugo (90272442)

# of Collaborated Projects: 6 results

# of Collaborated Products: 5 results
3. SUMIKOSHI Kazuya (90431832)

# of Collaborated Projects: 2 results

# of Collaborated Products: 0 results
4. NEGAMI Tatsuki

# of Collaborated Projects: 2 results

# of Collaborated Products: 11 results
5. 葛山智久 (30280952)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
6. 内山真伸 (00271916)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
7. 丸山千登勢 (20452120)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
8. 渡辺賢二 (50360938)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
9. 勝山陽平 (50646437)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
10. 山崎真巳 (70222370)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
11. 脇本敏幸 (70363900)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
12. 大栗博毅 (80311546)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
13. 淡川孝義 (80609834)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
14. 荘司長三 (90379587)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
15. 森脇由隆 (70751303)

# of Collaborated Projects: 1 results

# of Collaborated Products: 3 results
16. 藤田卓 (90962415)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
17. 山形敦史 (20463903)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
18. 難波康祐 (50414123)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
19. 村田佳子 (60256047)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results

Terada Toru 寺田 透

TERADA Tohru 寺田 透

Research Projects

Research Products

Co-Researchers

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Development of a method to predict substrate and reaction specificities using predicted structuresPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

A theoretical verification of the ligand-binding-pathway hypothesisPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

Multi-scale simulation of protein-ligand binding processPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

ミニ蛋白質に共通するフォールディング機構の解明Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

複合体形成に伴うタンパク質の立体構造変化パスウェイの予測・解析法の開発Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Terada Toru 寺田透

TERADA Tohru 寺田透