TSUKAMOTO Koki 塚本弘毅

Researcher Number	90399501
Affiliation (based on the past Project Information) *help	2010: 産業技術総合研究所, 生命情報工学研究センター, 特別研究員 2007: Computational Biology Research Center, Research Staff 2007: 産業技術総合研究所, 生命情報工学研究センター, 特別研究員 2006 – 2007: 独立行政法人産業技術総合研究所, 生命情報工学研究センター, 産総研特別研究員 2005: 独立行政法人産業技術総合研究所, 生命情報科学研究センター, 産総研特別研究員
Review Section/Research Field	Except Principal Investigator Bioinformatics/Life informatics
Keywords	Except Principal Investigator classification / enzyme reactions / enzyme active sites / protein structures / oxidoreductases / 水素化物イオン移動反応 / フラグメント分子軌道法 / 触媒機構分類 / 電子移動反応 / 分類学 … More / 酵素反応 / 酵素活性部位 / 蛋白質立体構造 / 酸化還元酵素 / バイオインフォマティクス / 高性能計算 / ドッキング / 蛋白質 / コンピュータシミュレーション Less

An exhaustive all-to-all protein-protein interaction prediction algorithm based on 3-D shape complimentarity and its statistical distribution on protein surface.
- Principal Investigator
  
  AKIYAMA Yutaka
- Project Period (FY)
  2007 – 2010
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Research Field
  
  Bioinformatics/Life informatics
- Research Institution
  Tokyo Institute of Technology
Systematic analyses and development of classification for catalytic mechanisms of oxidoreductase enzymes based on structural information
- Principal Investigator
  
  NAGANO Nozomi
- Project Period (FY)
  2005 – 2007
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Research Field
  
  Bioinformatics/Life informatics
- Research Institution
  National Institute of Advanced Industrial Science and Technology

All 2008 2007 2006

All Journal Article Presentation

[Journal Article] evaluation and prediction system by using the shape complementarity characteristic between proteins2008
- Author(s)
  Koki Tsukamoto, Tatsuya Yoshikawa, Yuichiro Hourai, Kazuhiko Fukui, Yutaka Akiyama, Development of an affinity
- Journal Title
  
  Journal of Bioinformatics and Computational Biology 6(6)
  
  Pages: 1133-1156
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19300102
[Journal Article] Development of an affinity evaluation and prediction system by using the shape complementarity characteristic between proteins2008
- Author(s)
  Koki Tsukamoto, Tatsuya Yoshikawa, Yuichiro Hourai, Kazuhiko Fukui, Yutaka Akiyama
- Journal Title
  
  Journal of Bioinformatics and Computational Biology 6(6)
  
  Pages: 1133-1156
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19300102
[Journal Article] Development of an affinity evaluation and prediction system by using the shape complementarity characteristic between proteins2008
- Author(s)
  Koki Tsukamoto, Tatsuya Yoshikawa, Yuichiro Hourai, Kazuhiko Fukui, Yutaka Akiyama
- Journal Title
  
  Journal of Bioinformatics and Computational Biology 6 (6)
  
  Pages: 1133-1156
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19300102
[Journal Article] Evaluation for interaction energy between glutamine and glutamine and various chemical compounds for developing the virtual screening system using quantum chemical calculations and molecular dynamics simulations.2007
- Author(s)
  K. Tsukamoto, H. Shimizu, T. Ishida, Y. Akiyama, N. Nukina
- Journal Title
  
  WSEAS Transactions on Computers 6(4)
  
  Pages: 636-641
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-17300097
[Journal Article] Evaluation for interaction energy between glutamine and glutamine and various chemical compounds for developing the virtual screening system using quantum chemical calculations and molecular dynamics simulations.2007
- Author(s)
  K.Tsukamoto, H.Shimizu, T.Ishida, Y.Akiyama, N.Nukina
- Journal Title
  
  WSEAS Transactions on Computers 6
  
  Pages: 636-641
- Description
  「研究成果報告書概要(和文)」より
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17300097
[Journal Article] Evaluation for interaction energy between glutamine and glutamine and various chemical compounds for developing the virtual screening system using quantum chemical calculations and molecular dynamics simulations.2007
- Author(s)
  K.Tsukamoto, H.Shimizu, T.Ishida, Y.Akiyama, N.Nukina
- Journal Title
  
  WSEAS Transactions on Computers 6(4)
  
  Pages: 636-641
- Data Source
  KAKENHI-PROJECT-17300097
[Journal Article] Automated Docking of NADH to the Active Site of Nitric Oxide Reductase from Fusarium Oxysporum and Semi-empirical Calculations of the Electron Transfer Mechanism and the Hydrogen-bonding Network.2006
- Author(s)
  K. Tsukamoto, Y. Akiyama
- Journal Title
  
  WSEAS Transactions on Computers 5(8)
  
  Pages: 1701-1706
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-17300097
[Journal Article] Aggrigation mechanism of polyglutamine diseases revealed using quantum chemical calculations, fragment molecular orbital calculations, molecular dynamics simulations, and binding free energy calculations2006
- Author(s)
  K.Tsukamoto, H.Shimizu, T.Ishida, Y.Akiyama, N.Nukina
- Journal Title
  
  Journal of Molecular Structure:THEOCHEM 778
  
  Pages: 85-95
- Description
  「研究成果報告書概要(和文)」より
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17300097
[Journal Article] Automated Docking of NADH to the Active Site of Nitric Oxide Reductase from Fusarium Oxysporum and Semi-empirical Calculations of the Electron Transfer Mechanism and the Hydrogen-bonding Network2006
- Author(s)
  K.Tsukamoto, Y.Akiyama
- Journal Title
  
  WSEAS Transactions on Computers 5(8)
  
  Pages: 1701-1706
- Data Source
  KAKENHI-PROJECT-17300097
[Journal Article] Aggrigation mechanism of polyglutamine diseases revealed using quantum chemical calculations, fragment molecular orbital calculations, molecular dynamics simulations, and binding free energy calculations.2006
- Author(s)
  K. Tsukamoto, H. Shimizu, T. Ishida, Y. Akiyama, N. Nukina
- Journal Title
  
  Journal of Molecular Structure : THEOCHEM 778
  
  Pages: 85-95
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-17300097
[Journal Article] Automated Docking of NADH to the Active Site of Nitric Oxide Reductase from Fusarium Oxysporum and Semi-empirical Calculations of the Electron Transfer Mechanism and the Hydrogen-bonding Network2006
- Author(s)
  K.Tsukamoto, Y.Akiyama
- Journal Title
  
  WSEAS Transactions on Computers 5
  
  Pages: 1701-1706
- Description
  「研究成果報告書概要(和文)」より
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17300097
[Journal Article] Aggrigation mechanism of polyglutamine diseases revealed using quantum chemical calculations, fragment molecular orbital calculations, molecular dynamics simulations, and binding free energy calculations2006
- Author(s)
  K.Tsukamoto, H.Shimizu, T.Ishida, Y.Akiyama, N.Nukina
- Journal Title
  
  Journal of Molecular Structure : THEOCHEM 778
  
  Pages: 85-95
- Data Source
  KAKENHI-PROJECT-17300097
[Presentation] Aggregation mechanism of polyglutamine diseases revealed using quantum chemical calculations, fragment molecular orbital calculations, molecular dynamics simulations, and binding free energy calculations2007
- Author(s)
  Koki Tsukamoto, Hideaki Shimizu, Takashi Ishida, Yutaka Akiyama, Nobuyuki Nukina
- Organizer
  The 2007 Annual Conference of Japanese Society for Bioinformatics (JSBi2007)
- Place of Presentation
  東京・お台場
- Year and Date
  2007-12-18
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-17300097
[Presentation] Aggregation mechanism of polyglutamine diseases revealed using quantum chemical calculations, fragment molecular orbital calculations, molecular dynamics simulations,and binding free energy calculations2007
- Author(s)
  Koki Tsukamoto, Hideaki Shimizu, Takashi Ishida,Yutaka Akiyama, Nobuyuki Nukina
- Organizer
  The 2007 Annual Conference of Japanse Society for Bioinformatics(JSBi2007)
- Place of Presentation
  Tokyo
- Year and Date
  2007-12-18
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-17300097
[Presentation] Aggiregation mechanism of polyglutamine diseases revealed using quantumchemical calculations,fragment molecular orbital calculations,molecular dvnamics simulations,and bindinff free energy calculations2007
- Author(s)
  Koki Tsukamoto, Hideaki Shimizu, Takashi Ishida, Yutaka Akiyama, Nobuyuki Nukina
- Organizer
  The 2007 Annual Conference of Japanese Society forBioinformatics (JSBi2007)
- Place of Presentation
  東京・お台場
- Year and Date
  2007-12-18
- Data Source
  KAKENHI-PROJECT-17300097

1. AKIYAMA Yutaka (30243091)

# of Collaborated Projects: 1 results

# of Collaborated Products: 3 results
2. NAGANO Nozomi (70357648)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results

TSUKAMOTO Koki 塚本 弘毅

Research Projects

Research Products

Co-Researchers

An exhaustive all-to-all protein-protein interaction prediction algorithm based on 3-D shape complimentarity and its statistical distribution on protein surface.

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

Systematic analyses and development of classification for catalytic mechanisms of oxidoreductase enzymes based on structural information

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

[Journal Article] evaluation and prediction system by using the shape complementarity characteristic between proteins2008

Author(s)

Journal Title

Data Source

[Journal Article] Development of an affinity evaluation and prediction system by using the shape complementarity characteristic between proteins2008

Author(s)

Journal Title

Data Source

[Journal Article] Development of an affinity evaluation and prediction system by using the shape complementarity characteristic between proteins2008

Author(s)

Journal Title

Data Source

[Journal Article] Evaluation for interaction energy between glutamine and glutamine and various chemical compounds for developing the virtual screening system using quantum chemical calculations and molecular dynamics simulations.2007

Author(s)

Journal Title

Description

Data Source

[Journal Article] Evaluation for interaction energy between glutamine and glutamine and various chemical compounds for developing the virtual screening system using quantum chemical calculations and molecular dynamics simulations.2007

Author(s)

Journal Title

Description

Data Source

[Journal Article] Evaluation for interaction energy between glutamine and glutamine and various chemical compounds for developing the virtual screening system using quantum chemical calculations and molecular dynamics simulations.2007

Author(s)

Journal Title

Data Source

[Journal Article] Automated Docking of NADH to the Active Site of Nitric Oxide Reductase from Fusarium Oxysporum and Semi-empirical Calculations of the Electron Transfer Mechanism and the Hydrogen-bonding Network.2006

Author(s)

Journal Title

Description

Data Source

[Journal Article] Aggrigation mechanism of polyglutamine diseases revealed using quantum chemical calculations, fragment molecular orbital calculations, molecular dynamics simulations, and binding free energy calculations2006

Author(s)

Journal Title

Description

Data Source

[Journal Article] Automated Docking of NADH to the Active Site of Nitric Oxide Reductase from Fusarium Oxysporum and Semi-empirical Calculations of the Electron Transfer Mechanism and the Hydrogen-bonding Network2006

Author(s)

Journal Title

Data Source

[Journal Article] Aggrigation mechanism of polyglutamine diseases revealed using quantum chemical calculations, fragment molecular orbital calculations, molecular dynamics simulations, and binding free energy calculations.2006

Author(s)

Journal Title

Description

Data Source

[Journal Article] Automated Docking of NADH to the Active Site of Nitric Oxide Reductase from Fusarium Oxysporum and Semi-empirical Calculations of the Electron Transfer Mechanism and the Hydrogen-bonding Network2006

Author(s)

Journal Title

Description

Data Source

[Journal Article] Aggrigation mechanism of polyglutamine diseases revealed using quantum chemical calculations, fragment molecular orbital calculations, molecular dynamics simulations, and binding free energy calculations2006

Author(s)

Journal Title

Data Source

[Presentation] Aggregation mechanism of polyglutamine diseases revealed using quantum chemical calculations, fragment molecular orbital calculations, molecular dynamics simulations, and binding free energy calculations2007

Author(s)

Organizer

Place of Presentation

Year and Date

Description

Data Source

[Presentation] Aggregation mechanism of polyglutamine diseases revealed using quantum chemical calculations, fragment molecular orbital calculations, molecular dynamics simulations,and binding free energy calculations2007

Author(s)

Organizer

TSUKAMOTO Koki 塚本弘毅