Yoda Takao 依田隆夫

… Alternative Names

依田隆夫ヨダタカオ

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Researcher Number	50367900
Other IDs
Affiliation (Current)	2022: 長浜バイオ大学, バイオサイエンス学部, 准教授
Affiliation (based on the past Project Information) *help	2021 – 2022: 長浜バイオ大学, バイオサイエンス学部, 准教授 2014 – 2015: 長浜バイオ大学, バイオサイエンス学部, 准教授 2013: 長浜バイオ大学, バイオサイエンス学部, 講師 2004 – 2007: 長浜バイオ大学, バイオサイエンス学部, 講師
Review Section/Research Field	Principal Investigator Science and Engineering / Life / Health / Medical informatics / Transformative Research Areas, Section (III) / Basic Section 43020:Structural biochemistry-related Except Principal Investigator Transformative Research Areas, Section (III)
Keywords	Principal Investigator 分子動力学シミュレーション / 分子シミュレーション / 拡張アンサンブル法 / タンパク質 / ペプチド / βヘアピン / 二次構造形成 / コンピューターシミュレーション / フオールデイング / 2次構造 … More / 二次構造 / 折れ畳み / ターン構造 / 抗菌ペプチド / 分子動力学法 / シミュレーション / 天然変性蛋白質 / 長鎖ノンコーディングRNA / Hero蛋白質 / 抗微生物ペプチド … More Except Principal Investigator lncRNA / 超天然変性タンパク質 / ノンコーディングRNA / 天然変性領域 Less

Management of non-domain biopolymer research group
- Principal Investigator
  
  中川真一
- Project Period (FY)
  2021 – 2025
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (A)
- Review Section
  
  Transformative Research Areas, Section (III)
- Research Institution
  Hokkaido University
非ドメイン型バイオポリマーの分子動力学計算Principal Investigator
- Principal Investigator
  
  依田隆夫
- Project Period (FY)
  2021 – 2025
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (A)
- Review Section
  
  Transformative Research Areas, Section (III)
- Research Institution
  Nagahama Institute of Bio-Science and Technology
抗微生物ペプチドCryptdin-4多量体の膜透過過程と活性機構の解明Principal Investigator
- Principal Investigator
  
  依田隆夫
- Project Period (FY)
  2021 – 2023
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Review Section
  
  Basic Section 43020:Structural biochemistry-related
- Research Institution
  Nagahama Institute of Bio-Science and Technology
Simulation study on functions of an anti-microbial peptidePrincipal Investigator
- Principal Investigator
  
  Yoda Takao
- Project Period (FY)
  2013 – 2015
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Research Field
  
  Life / Health / Medical informatics
- Research Institution
  Nagahama Institute of Bio-Science and Technology
分子シミュレーションによる2次構造形成過程の研究Principal Investigator
- Principal Investigator
  
  依田隆夫
- Project Period (FY)
  2006 – 2007
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Review Section
  
  Science and Engineering
- Research Institution
  Nagahama Institute of Bio-Science and Technology
拡張アンサンブル法による蛋白質部分配列ペプチドの構造空間探索Principal Investigator
- Principal Investigator
  
  依田隆夫
- Project Period (FY)
  2004 – 2005
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Review Section
  
  Science and Engineering
- Research Institution
  Nagahama Institute of Bio-Science and Technology

All 2022 2021 2015 2014 2007 2006 2005 2004

All Journal Article Presentation

[Journal Article] Intermolecular Interactions between a Membrane Protein and a Glycolipid Essential for Membrane Protein Integration2022
- Author(s)
  Mori Shoko、Nomura Kaoru、Fujikawa Kohki、Osawa Tsukiho、Shionyu Masafumi、Yoda Takao、Shirai Tsuyoshi、Tsuda Shugo、Yoshizawa-Kumagaye Kumiko、Masuda Shun、Nishio Hideki、Yoshiya Taku、Suzuki Sonomi、Muramoto Maki、Nishiyama Ken-ichi、Shimamoto Keiko
- Journal Title
  
  ACS Chemical Biology
  
  Volume: 17 Pages: 609-618
- DOI
  10.1021/acschembio.1c00882
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19K12211, KAKENHI-PROJECT-19H02843, KAKENHI-PROJECT-21H03547, KAKENHI-PROJECT-20K05738, KAKENHI-PROJECT-21K06037
[Journal Article] Deciphering Supramolecular Structures with Protein-Protein Interaction Network Modeling.2015
- Author(s)
  Toshiyuki Tsuji, Takao Yoda, and Tsuyoshi Shirai
- Journal Title
  
  Scientific Reports
  
  Volume: 5 Pages: 16341-16341
- DOI
  10.1038/srep16341
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-PROJECT-25330355, KAKENHI-PROJECT-24370046, KAKENHI-PROJECT-25280109
[Journal Article] GENESIS: A hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations2015
- Author(s)
  Jung, J., Mori, T., Kobayashi, C., Matsunaga, Y., Yoda, T., Feig, M., Sugita, Y.
- Journal Title
  
  WIREs; Comput. Mol. Sci.
  
  Volume: -
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-25330355
[Journal Article] Salt effects on hydrophobic-core formation in folding of a helical mini protein studied by molecular dynamics simulations2014
- Author(s)
  T. Yoda, Y. Sugita, and Y. Okamoto
- Journal Title
  
  Proteins
  
  Volume: 82 Pages: 933-943
- DOI
  10.1002/prot.24467
- Peer Reviewed
- Data Source
  KAKENHI-ORGANIZER-25102001, KAKENHI-PLANNED-25102009, KAKENHI-PROJECT-25247071, KAKENHI-PROJECT-25330355
[Journal Article] Cooperative folding mechanism of a β-hairpin peptide studied by a multicanonical replica-exchange molecular dynamics simulation2007
- Author(s)
  Yoda, T., Sugita, Y., Okamoto, Y.
- Journal Title
  
  Proteins : Structure, Function, and Bioinformatics 66・4
  
  Pages: 846-859
- Data Source
  KAKENHI-PROJECT-18031037
[Journal Article] Replica-exchange molecular dynamics simulation of diffracted X-ray tracking2007
- Author(s)
  Y. Kawashima, Y.C. Sasaki, Y. Sugita, T. Yoda, Y. Okamoto,
- Journal Title
  
  Molecular Simulation 33
  
  Pages: 97-102
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-18031037
[Journal Article] Structural changes in the cytoplasmic domain of phospholamban by phosphorylation at Ser16 : A molecular dynamics study2006
- Author(s)
  Sugita, Y., Miyashita, N., Yoda, T., Ikeguchi, M., Toyoshima, C
- Journal Title
  
  Biochemistry 45・39
  
  Pages: 11752-11761
- Data Source
  KAKENHI-PROJECT-18031037
[Journal Article] Effects of the fixed end in single-molecule imaging techniques : A replica-exchange molecular dynamics simulation study2005
- Author(s)
  Y.Kawashima, Y.Sugita, T.Yoda, Y.Okamoto
- Journal Title
  
  Chem.Phys.Lett. 414
  
  Pages: 449-455
- Data Source
  KAKENHI-PROJECT-16041241
[Journal Article] Structures of a peptide fragment of b2-microglobulin studied by replica-exchange molecular dynamics simulations - Towards the understanding of the mechanism of amyloid formation2005
- Author(s)
  M.Nishino, Y.Sugita, Y.Yoda, Y.Okamoto
- Journal Title
  
  FEBS lett., 579
  
  Pages: 5425-5429
- Data Source
  KAKENHI-PROJECT-16041241
[Journal Article] Secondary-structure preferences of force fields for proteins evaluated by generalized-ensemble simulations2004
- Author(s)
  Yoda, T., Sugita, Y., Okanmoto, Y.
- Journal Title
  
  Chemical Physics 307
  
  Pages: 269-283
- Data Source
  KAKENHI-PROJECT-16041241
[Presentation] Conformations and distributions of Cryptdin-4, lipids, and water observed in membrane self-assembly molecular dynamics simulations2021
- Author(s)
  依田隆夫
- Organizer
  日本生物物理学会第59回年会
- Data Source
  KAKENHI-PROJECT-21K06037
[Presentation] Simulation Study on Conformations of Antimicrobial Peptide Cryptdin 4 and its Mutants2015
- Author(s)
  Takao Yoda
- Organizer
  2nd International Symposium on Computational Materials and Biological Sciences
- Place of Presentation
  名古屋大学
- Year and Date
  2015-09-01
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25330355
[Presentation] Salt effects on folding of a helical mini protein villin headpiece subdomain HP36 studied by generalized-ensemble simulations2014
- Author(s)
  Takao Yoda, Yuji Sugita, and Yuko Okamoto
- Organizer
  Biophysical Society 58th Annual Meeting
- Place of Presentation
  Moscone Center, San Francisco CA.
- Data Source
  KAKENHI-PROJECT-25330355
[Presentation] 抗菌ペプチド Cryptdin-4 ジスルフィド結合変異体の分子動力学シミュレーション2014
- Author(s)
  依田隆夫，辻敏之，杉田有治
- Organizer
  第14回日本蛋白質科学会年会
- Place of Presentation
  ワークピア横浜／横浜産貿ホールマリネリア
- Year and Date
  2014-06-27
- Data Source
  KAKENHI-PROJECT-25330355
[Presentation] Simulation Study on Conformations of Small Peptides.2014
- Author(s)
  Takao Yoda
- Organizer
  Dushanbe Symposium on Computational Materials and Biological Sciences 2014
- Place of Presentation
  S.U. Umarov Physical-Technical Institute of the Academy of Sciences of the Republic of Tajikistan
- Year and Date
  2014-09-24
- Invited
- Data Source
  KAKENHI-PROJECT-25330355

1. 中川真一 (50324679)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
2. 廣瀬哲郎 (30273220)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
3. 尾山大明 (30422398)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
4. 稲田利文 (40242812)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
5. 荒川和晴 (40453550)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
6. 甲斐歳恵 (40579786)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
7. 伊藤拓宏 (70401164)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
8. 泊幸秀 (90447368)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
9. 鄭載運 (10554701)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
10. 譚丞 (20865886)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
11. SHIONYU Masafumi

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
12. 白井剛

# of Collaborated Projects: 0 results

# of Collaborated Products: 2 results
13. 岡本祐幸

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
14. 島本啓子

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
15. 藤川紘樹

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

Yoda Takao 依田 隆夫

依田 隆夫 ヨダ タカオ

Research Projects

Research Products

Co-Researchers

Management of non-domain biopolymer research group

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

非ドメイン型バイオポリマーの分子動力学計算Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

抗微生物ペプチドCryptdin-4多量体の膜透過過程と活性機構の解明Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Simulation study on functions of an anti-microbial peptidePrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

分子シミュレーションによる2次構造形成過程の研究Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

拡張アンサンブル法による蛋白質部分配列ペプチドの構造空間探索Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

[Journal Article] Intermolecular Interactions between a Membrane Protein and a Glycolipid Essential for Membrane Protein Integration2022

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Deciphering Supramolecular Structures with Protein-Protein Interaction Network Modeling.2015

Author(s)

Journal Title

DOI

Data Source

[Journal Article] GENESIS: A hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations2015

Author(s)

Journal Title

Data Source

[Journal Article] Salt effects on hydrophobic-core formation in folding of a helical mini protein studied by molecular dynamics simulations2014

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Cooperative folding mechanism of a β-hairpin peptide studied by a multicanonical replica-exchange molecular dynamics simulation2007

Author(s)

Journal Title

Data Source

[Journal Article] Replica-exchange molecular dynamics simulation of diffracted X-ray tracking2007

Author(s)

Journal Title

Data Source

[Journal Article] Structural changes in the cytoplasmic domain of phospholamban by phosphorylation at Ser16 : A molecular dynamics study2006

Author(s)

Journal Title

Data Source

[Journal Article] Effects of the fixed end in single-molecule imaging techniques : A replica-exchange molecular dynamics simulation study2005

Author(s)

Journal Title

Data Source

[Journal Article] Structures of a peptide fragment of b2-microglobulin studied by replica-exchange molecular dynamics simulations - Towards the understanding of the mechanism of amyloid formation2005

Author(s)

Journal Title

Data Source

Yoda Takao 依田隆夫

依田隆夫ヨダタカオ