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Molecualr dynamics study on the molecuar permeability of membrane protein

Research Project

Project/Area Number 23750008
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Physical chemistry
Research InstitutionKanazawa University

Principal Investigator

SAITO Hiroaki  金沢大学, 数物科学系, 助教 (40506820)

Project Period (FY) 2011 – 2013
Project Status Completed (Fiscal Year 2013)
Budget Amount *help
¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Fiscal Year 2013: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2012: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2011: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Keywords分子動力学法 / 脂質二重層膜 / 膜タンパク質 / 自由エネルギー / ペプチド / イオンチャネル / 溶媒和自由エネルギー / 分子動力学 / グラミシジン
Research Abstract

We have carried out molecular dynamics simulations to analysis the structure and dynamics of peptide and membrane protein in several lipid bilayer environments and have investigated the ion and molecular permeability through the channel of membrane protein. The thermal stability of membrane protein in the lipid bilayers has also been investigated by free energy calculation.

Report

(4 results)
  • 2013 Annual Research Report   Final Research Report ( PDF )
  • 2012 Research-status Report
  • 2011 Research-status Report
  • Research Products

    (141 results)

All 2014 2013 2012 2011 Other

All Journal Article (59 results) (of which Peer Reviewed: 59 results,  Open Access: 1 results) Presentation (82 results) (of which Invited: 3 results)

  • [Journal Article] Analysis of water molecules around GTP in Hras-GTP complex and GDP in Hras-GDP complex by molecular dynamics simulations2014

    • Author(s)
      Takeshi Miyakawa, Ryota Morikawa, Masako Takasu, Kimikazu Sugimori, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
    • Journal Title

      Mol. Phys

      Volume: 112 Pages: 526-532

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Network of water molecules around guanine nucleotide in the Hras-GTP and-GDP complexes by MD simulations2014

    • Author(s)
      Takeshi Miyakawa, Ryota Morikawa, Masako Takasu, Kimikazu Sugimori, Tomokazu Kawaguchi, Hiroaki Saito, Hidemi Nagao
    • Journal Title

      JPS Conf. Proc

      Volume: 016006

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Study of Gramicidin A in Lipid Bilayer : Electrostatic Map and Ion Conduction2014

    • Author(s)
      Hiroaki SAITO, Masashi IWAYAMA, Kazutomo KAWAGUCHI, Taku MIZUKAMI, Takeshi MIYAKAWA, Masako TAKASU, and Hidemi NAGAO
    • Journal Title

      JPS Conf. Proc

      Volume: 012053

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Study of Hsp90 and ADP : Hydrogen Bond Analysis for ADP Dissociation2014

    • Author(s)
      Kazutomo KAWAGUCHI, Hiroaki SAITO, Hidemi NAGAO
    • Journal Title

      JPS Conf. Proc

      Volume: 012056

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Protein--protein interactions of Azurin complex in liquid system2014

    • Author(s)
      Micke Rusmerryani, Masako Takasu, Kazutomo Kawaguchi, Hiroaki Saito, and Hidemi Nagao
    • Journal Title

      JPS Conf. Proc

      Volume: 012054

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Π-stacking Interaction between Heterocyclic Rings in a Reaction Field of Biological System2014

    • Author(s)
      Muhamad KOYIMATU, Hideto SHIMAHARA, Kimikazu SUGIMORI, Kazutomo KAWAGUCHI, Hiroaki SAITO, and Hidemi NAGAO
    • Journal Title

      JPS Conf. Proc

      Volume: 012055

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Analysis of water molecules around GTP in Hras-GTP complex and GDP in Hras-GDP complex by molecular dynamics simulations2014

    • Author(s)
      T. Miyakawa
    • Journal Title

      MOLECULAR PHYSICS

      Volume: 112 Issue: 3-4 Pages: 526-532

    • DOI

      10.1080/00268976.2013.852697

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Network of water molecules around guanine nucleotide in the Hras-GTP and -GDP complexes by MD simulations2014

    • Author(s)
      Takeshi Miyakawa, Ryota Morikawa, Masako Takasu, Kimikazu Sugimori, Tomokazu Kawaguchi, Hiroaki Saito, Hidemi Nagao
    • Journal Title

      JPS Conf. Proc.

      Volume: volume 1 Pages: 16006-16006

    • DOI

      10.7566/jpscp.1.016006

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Study of Gramicidin A in Lipid Bilayer: Electrostatic Map and Ion Conduction2014

    • Author(s)
      Hiroaki SAITO, Masashi IWAYAMA, Kazutomo KAWAGUCHI, Taku MIZUKAMI, Takeshi MIYAKAWA, Masako TAKASU, and Hidemi NAGAO
    • Journal Title

      JPS Conf. Proc

      Volume: volume 1 Pages: 012053-012053

    • DOI

      10.7566/jpscp.1.012053

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Molecular Dynamics Study of Hsp90 and ADP: Hydrogen Bond Analysis for ADP Dissociation2014

    • Author(s)
      Kazutomo KAWAGUCHI, Hiroaki SAITO, Hidemi NAGAO
    • Journal Title

      JPS Conf. Proc.

      Volume: volume 1 Pages: 012056-012056

    • DOI

      10.7566/jpscp.1.012056

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Protein--protein interactions of Azurin complex in liquid system2014

    • Author(s)
      Micke Rusmerryani, Masako Takasu, Kazutomo Kawaguchi, Hiroaki Saito, and Hidemi Nagao
    • Journal Title

      JPS Conf. Proc.

      Volume: volume 1

    • DOI

      10.7566/jpscp.1.012054

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Π-stacking Interaction between Heterocyclic Rings in a Reaction Field of Biological System2014

    • Author(s)
      Muhamad KOYIMATU, Hideto SHIMAHARA, Kimikazu SUGIMORI, Kazutomo KAWAGUCHI, Hiroaki SAITO, and Hidemi NAGAO
    • Journal Title

      JPS Conf. Proc.

      Volume: volume 1

    • DOI

      10.7566/jpscp.1.012055

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular dynamics study on the free energy profile for dissociation of ADP from N-terminal domain of Hsp902013

    • Author(s)
      Kazutomo Kawaguchi, Hiroaki Saito, Susumu Okazaki, Hidemi Nagao
    • Journal Title

      Chem. Phys. Lett

      Volume: 588 Pages: 226-230

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Simulations of the Hras-GTP complex and the Hras-GDP complex2013

    • Author(s)
      Takeshi Miyakawa, Ryota Morikawa, Masako Takasu, Kimikazu Sugimori, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
    • Journal Title

      Int. J. Quantum Chem

      Volume: 113 Pages: 2333-2337

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Study on Binding Free Energy of Azurin?Cytochrome c551 Complex2013

    • Author(s)
      Hiroaki Saito, Masashi Iwayama, Taku Mizukami, Jiyoung Kang, Masaru Tateno, Hidemi Nagao
    • Journal Title

      Chem. Phys. Lett

      Volume: 556 Pages: 297-302

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Computational Study of Oxidation Potential of Ketone Molecule2013

    • Author(s)
      Isman Kurniawan, Hiroaki Saito, Kazuto Kawaguchi, Hidemi Nagao
    • Journal Title

      Recent Development in Computational Science

      Volume: 4 Pages: 45-52

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structure and Hydration Free Energy of Ketone Compound in Neutral and Cationic State by Molecular Dynamics Simulation2013

    • Author(s)
      Masashi Iwayama, Kazutomo Kawaguchi, Hiroaki Saito and Hidemi Nagao
    • Journal Title

      Recent Development in Computational Science

      Volume: 4 Pages: 59-70

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Binding Free Energy of Protein-Ligand by Combining Docking and MD Simulation : A Comparison of Calculation Methods2013

    • Author(s)
      Meidy Triana Pakpahan, Hiroaki Saito, Kazutomo Kawaguchi, Hidemi Nagao
    • Journal Title

      Recent Development in Computational Science

      Volume: 4 Pages: 71-78

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Coarse-grained Simulation of Azurin Crystal Complex System : Protein-protein Interactions2013

    • Author(s)
      Micke Rusmerryani, Masako Takasu, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
    • Journal Title

      Recent Development in Computational Science

      Volume: 4 Pages: 79-86

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Theoretical study of a π-stacking interaction in carbonic anhydrase2013

    • Author(s)
      Muhamad Koyimatu, Hideto Shimahara, Kazutomo Kawaguchi, Hirosaki Saito, Kimikazu Sugimori, Hidemi Nagao
    • Journal Title

      Recent Development in Computational Science

      Volume: 4 Pages: 87-94

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Analysis of water molecules in the Hras-GTP and GDP complexes with molecular dynamics simulations2013

    • Author(s)
      T. Miyakawa, R. Morikawa, M. Takasu, K. Sugimori, K. Kawaguchi, H. Saito and Hidemi Nagao
    • Journal Title

      Progress in Theoretical Chemistry and Physics

      Volume: 27 Pages: 351-360

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular dynamics study on the free energy profile for dissociation of ADP from N-terminal domain of Hsp902013

    • Author(s)
      Kazutomo Kawaguchi, Hiroaki Saito, Susumu Okazaki, Hidemi Nagao
    • Journal Title

      Chem. Phys. Lett.

      Volume: 588 Pages: 226-230

    • DOI

      10.1016/j.cplett.2013.10.015

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Simulations of the Hras-GTP complex and the Hras-GDP complex2013

    • Author(s)
      Takeshi Miyakawa, Ryota Morikawa, Masako Takasu, Kimikazu Sugimori, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
    • Journal Title

      Int. J. Quantum Chem.

      Volume: 113 Issue: 21 Pages: 2333-2337

    • DOI

      10.1002/qua.24457

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Study of Electrostatic Potential along Lipid Bilayer with Gramicidin A2013

    • Author(s)
      Hiroaki Saito, Megumi Nishimura, Hiroyuki Takagi, Takeshi Miyakawa, Kazutomo Kawaguchi, Hidemi Nagao
    • Journal Title

      AIP Conf. Proc.

      Volume: 1518 Pages: 633-636

    • DOI

      10.1063/1.4794649

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Evaluation of scoring functions for protein-ligand docking2013

    • Author(s)
      Meidy T. Pakpahan, Micke Rusmerryani, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
    • Journal Title

      AIP Conf. Proc.

      Volume: 1518 Pages: 645-648

    • DOI

      10.1063/1.4794652

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Transition State Analysis of Azurin via Go-like Model2013

    • Author(s)
      Micke Rusmerryani, Meidy T. Pakpahan, Megumi Nishimura, Masako Takasu, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
    • Journal Title

      AIP Conf. Proc.

      Volume: 1518 Pages: 641-644

    • DOI

      10.1063/1.4794651

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Theoretical Study on Entrainment Phenomenon in Model Molecular Systems2013

    • Author(s)
      H. Nagao, S. Kawamoto, M. Rusmerryani, A. Purqon, K. Kawaguchi, H. Saito
    • Journal Title

      AIP Conference Proceedings

      Volume: 1518 Pages: 729-732

    • DOI

      10.1063/1.4794669

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Conformational Stability of Met20 Loop of DHFR:A molecular Dynamics Study2013

    • Author(s)
      Megumi Nishimura, Hiroaki Saito, Kazutomo Kawaguchi, Hidemi Nagao
    • Journal Title

      AIP Conf. Proc.

      Volume: 1518 Pages: 654-657

    • DOI

      10.1063/1.4794654

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Molecular dynamics studies of Hsp90 with ADP: protein-ligand binding dynamics2013

    • Author(s)
      Kazutomo Kawaguchi, Hiroyuki Takagi, Masako Takasu, Hiroaki Saito, Hidemi Nagao
    • Journal Title

      AIP Conf. Proc.

      Volume: 1518 Pages: 637-640

    • DOI

      10.1063/1.4794650

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Theoretical Model for Assessing Properties of Local Structures in Metalloprotein2013

    • Author(s)
      Muhamad Koyimatu, Hideto Shimahara, Masashi Iwayama, Kimikazu Sugimori, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
    • Journal Title

      AIP Conf. Proc.

      Volume: 1518 Pages: 626-629

    • DOI

      10.1063/1.4794647

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] A molecular dynamics study of Hras-GTP and GDP complexes: the properties of water molecules around guanine nucleotide2013

    • Author(s)
      T. Miyakawa, R. Morikawa, M. Takasu, K. Sugimori, K. Kawaguchi, H. Saito, H. Nagao
    • Journal Title

      AIP Conf. Proc.

      Volume: 1518 Pages: 594-597

    • DOI

      10.1063/1.4794639

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Molecular dynamics analyses of the dissociation process of ADP from Hsp902012

    • Author(s)
      Kazutomo Kawaguchi, Hiroyuki Takagi, Masashi Iwayama, Takeshi Miyakawa, Hiroaki Saito, Masako Takasu, Hidemi Nagao
    • Journal Title

      Int. J. Quantum Chem

      Volume: 112 Pages: 3791-3795

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular dynamics study of gramicidin a in lipid bilayer : Structure and lateral pressure profile2012

    • Author(s)
      Hiroaki Saito, Masashi Iwayama, Hiroyuki Takagi, Megumi Nishimura, Takeshi Miyakawa, Kazutomo Kawaguchi, Masako Takasu, Taku Mizukami, H. Nagao
    • Journal Title

      Int. J. Quantum Chem

      Volume: 112 Pages: 3834-3839

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular dynamics studies of lipid bilayer with gramicidin A : effects of gramicidin A on membrane structure and hydrophobic match2012

    • Author(s)
      Hiroaki Saito, Taku Mizukami, Shuhei Kawamoto, Takeshi Miyakawa, Masashi Iwayama, Masako Takasu, Hidemi Nagao
    • Journal Title

      Int. J. Quantum Chem

      Volume: 112 Pages: 161-170

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Solvation effect on the structural change of globular protein : a molecular dynamics study2012

    • Author(s)
      Taku Mizukami, Hiroaki Saito, Shuhei Kawamoto, Takeshi Miyakawa, Masako Takasu, Hidemi Nagao
    • Journal Title

      Int. J. Quantum Chem

      Volume: 112 Pages: 344-350

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Cell penetrating peptide induces various deformations of lipid bilayer membrane : inverted micelle, double bilayer and trans-membrane2012

    • Author(s)
      Shuhei Kawamoto, Takeshi Miyakawa, Masako Takasu, Ryota Morikawa, Tatsuki Oda, Hiroaki Saito, Shiroh Futaki, Hidemi Nagao
    • Journal Title

      Int. J. Quantum Chem

      Volume: 112 Pages: 178-183

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] The potentials of the atoms around Mg2+ in the H-ras GTP complex and in the H-ras GDP complex2012

    • Author(s)
      T. Miyakawa, R. Morikawa, M. Takasu, K. Sugimori, K. Kawaguchi, H. Saito and Hidemi Nagao
    • Journal Title

      Progress in Theoretical Chemistry and Physics

      Volume: 26 Pages: 525-543

    • Related Report
      2013 Final Research Report 2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Free energy of cell-penetrating peptide through lipid bilayer membrane : coarse-grained model simulation2012

    • Author(s)
      S. Kawamoto, M. Takasu, T. Miyakawa, T. Oda, H. Saito, S. Futaki, H. Nagao, W. Shinoda
    • Journal Title

      Progress in Theoretical Chemistry and Physics

      Volume: 26 Pages: 503-511

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Study of Glutathione S-transferase : Structure and Binding Character of Glutathione2012

    • Author(s)
      Y. Omae, H. Saito, H. Takagi, M. Nishimura, M. Iwayama, K. Kawaguchi, H. Nagao
    • Journal Title

      Progress in Theoretical Chemistry and Physics

      Volume: 26 Pages: 545-553

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Temperature Effects on Dynamics of Spherical Micelles : A Molecular Dynamics Study2012

    • Author(s)
      Gia Septiana Wulandari, Micke Rusmerryani, Shuhei Kawamoto, Hiroaki Saito, Kiyoshi Nishikawa, Hidemi Nagao
    • Journal Title

      Recent Development in Computational Science

      Volume: 2 Pages: 59-68

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Studies on Structure and Dynamics of Spherical Micelles2012

    • Author(s)
      Micke Rusmerryani, Gia Septiana Wulandari, Shuhei Kawamoto, Hiroaki Saito, Kiyoshi Nishikawa, Hidemi Nagao
    • Journal Title

      Recent Development in Computational Science

      Volume: 2 Pages: 69-77

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Study on Binding Free Energy of Azurin-Cytochrome c551 Complex2012

    • Author(s)
      H. Saito, M. Iwayama, T. Mizukami, J. Kang, M.Tateno, H. Nagao
    • Journal Title

      Chemical Physics Letters

      Volume: 556 Pages: 297-302

    • DOI

      10.1016/j.cplett.2012.12.016

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Analyses of the Dissociation Process of ADP from Hsp902012

    • Author(s)
      K. Kawaguchi, H. Takagi, M. Iwayama, M.Nishimura, T. Miyakawa, H. Saito, M. Takasu, H.Nagao
    • Journal Title

      International Journal of Quantum Chemistry

      Volume: 112 Issue: 24 Pages: 3791-3795

    • DOI

      10.1002/qua.24229

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Study of Gramicidin A in Lipid Bilayer: Structure and Lateral Pressure Profile2012

    • Author(s)
      H. Saito, M. Iwayama, H. Takagi, M. Nishimura, T. Miyakawa, K. Kawaguchi, M. Takasu, T. Mizukami, H. Nagao
    • Journal Title

      International Journal of Quantum Chemistry

      Volume: 112 Issue: 24 Pages: 3834-3839

    • DOI

      10.1002/qua.24248

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Free energy of cell-penetrating peptide through lipid bilayer membrane: coarse-grained model simulation2012

    • Author(s)
      S. Kawamoto, M. Takasu, T. Miyakawa, T. Oda, H. Saito, S. Futaki, H. Nagao, W. Shinoda
    • Journal Title

      Progress in Theoretical Chemistry and Physics

      Volume: 26 Pages: 503-511

    • DOI

      10.1007/978-94-007-5297-9_29

    • ISBN
      9789400752962, 9789400752979
    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Study of Glutathione S-transferase: Structure and Binding Character of Glutathione2012

    • Author(s)
      Y. Omae, H. Saito, H. Takagi, M. Nishimura, M. Iwayama, K. Kawaguchi, H. Nagao
    • Journal Title

      Progress in Theoretical Chemistry and Physics

      Volume: 26 Pages: 545-553

    • DOI

      10.1007/978-94-007-5297-9_32

    • ISBN
      9789400752962, 9789400752979
    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Studies of Lipid Bilayer with Gramicidin A: Effects of Gramicidin A on Membrane Structure and Hydrophobic Match2012

    • Author(s)
      Hiroaki Saito, Taku Mizukami, Shuhei Kawamoto, Takeshi Miyakawa, Masashi Iwayama, Masako Takasu, Hidemi Nagao
    • Journal Title

      International Journal of Quantum Chemistry

      Volume: 112 Issue: 1 Pages: 161-170

    • DOI

      10.1002/qua.23252

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Solvation Effect on the Structural Change of Globular Protein: A Molecular Dynamics Study2012

    • Author(s)
      Taku Mizukami, Hiroaki Saito, Shuhei Kawamoto,Takeshi Miyakawa, Masashi Iwayama, Masako Takasu, Hidemi Nagao
    • Journal Title

      International Journal of Quantum Chemistry

      Volume: 112 Issue: 1 Pages: 344-350

    • DOI

      10.1002/qua.23251

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Cell-Penetrating Peptide Induces Various Deformations of Lipid Bilayer Membrane: Inverted Micelle,Double Bilayer, and Transmembrane2012

    • Author(s)
      Shuhei Kawamoto, Takeshi Miyakawa, Masako Takasu, Ryota Morikawa, Tatsuki Oda, Shiroh Futaki, Hidemi Nagao
    • Journal Title

      International Journal of Quantum Chemistry

      Volume: 112 Issue: 1 Pages: 178-183

    • DOI

      10.1002/qua.23177

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Cholesterol Effect on Water Permeability through DPPC and PSM Lipid Bilayers : A Molecular Dynamics Study2011

    • Author(s)
      Hiroaki Saito, Wataru Shinoda
    • Journal Title

      J. Phys. Chem. B

      Volume: 115 Pages: 15241-15250

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Cholesterol Effect on Water Permeability through DPPC and PSM Lipid Bilayers : A Molecular Dynamics Study2011

    • Author(s)
      斎藤大明、篠田渉
    • Journal Title

      Journal of Physical Chemistry B

      Volume: 115 Issue: 51 Pages: 15241-15250

    • DOI

      10.1021/jp201611p

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Study of Electrostatic Potential along Lipid Bilayer with Gramicidin A

    • Author(s)
      Hiroaki Saito, Megumi Nishimura, Hiroyuki Takagi, Takeshi Miyakawa, Kazutomo Kawaguchi, Hidemi Nagao
    • Journal Title

      AIP Conf. Proc

      Volume: 1518 Pages: 633-636

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Evaluation of scoring functions for protein-ligand docking

    • Author(s)
      Meidy T. Pakpahan, Micke Rusmerryani, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
    • Journal Title

      AIP Conf. Proc

      Volume: 1518 Pages: 645-648

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Transition State Analysis of Azurin via Go-like Model

    • Author(s)
      Micke Rusmerryani, Meidy T. Pakpahan, Megumi Nishimura, Masako Takasu, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
    • Journal Title

      AIP Conf. Proc

      Volume: 1518 Pages: 641-644

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Study on Entrainment Phenomenon in Model Molecular Systems

    • Author(s)
      Hidemi Nagao, Michke Rusmerryani, Acep Purqon, Kazutomo Kawaguchi, Hiroaki Saito
    • Journal Title

      AIP Conf. Proc

      Volume: 1518 Pages: 729-732

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Conformational Stability of Met20 Loop of DHFR : A molecular Dynamics Study

    • Author(s)
      Megumi Nishimura, Hiroaki Saito, Kazutomo Kawaguchi, Hidemi Nagao
    • Journal Title

      AIP Conf. Proc

      Volume: 1518 Pages: 654-657

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular dynamics studies of Hsp90 with ADP : protein-ligand binding dynamics

    • Author(s)
      Kazutomo Kawaguchi, Hiroyuki Takagi, Masako Takasu, Hiroaki Saito, Hidemi Nagao
    • Journal Title

      AIP Conf. Proc

      Volume: 1518 Pages: 637-640

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Theoretical Model for Assessing Properties of Local Structures in Metalloprotein

    • Author(s)
      Muhamad Koyimatu, Hideto Shimahara, Masashi Iwayama, Kimikazu Sugimori, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
    • Journal Title

      AIP Conf. Proc

      Volume: 1518 Pages: 626-629

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] A molecular dynamics study of Hras-GTP and GDP complexes : the properties of water molecules around guanine nucleotide

    • Author(s)
      T. Miyakawa, R. Morikawa, M. Takasu, K. Sugimori, K. Kawaguchi, H. Saito, H. Nagao
    • Journal Title

      AIP Conf. Proc

      Volume: 1518 Pages: 594-597

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Presentation] Thermal Stability of Gramicidin A in Lipid Bilayer: A Free Energy Analysis2014

    • Author(s)
      Hiroaki Saito, Masashi Iwayama, Kazutomo Kawaguchi, Taku Mizukami, Takeshi Miyakawa, Masako Takasu, and Hidemi Nagao
    • Organizer
      The 54th Sanibel Symposium
    • Place of Presentation
      Florida, USA
    • Related Report
      2013 Annual Research Report
  • [Presentation] Analysis of the site-dipole fields around guanine nucleotides in the Hras-GTP and Hras-GDP complexes2014

    • Author(s)
      Takeshi Miyakawa, Ryota Morikawa, Masako Takasu, Kimikazu Sugimori, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
    • Organizer
      The 54th Sanibel Symposium
    • Place of Presentation
      Florida, USA
    • Related Report
      2013 Annual Research Report
  • [Presentation] Hras-GTP/GDP の GTP/GDP周辺にある水分子水素結合場の分子動力学法による研究2014

    • Author(s)
      宮川毅, 森河良太, 高須昌子, 杉森公一,川口一朋, 齋藤大明, 長尾秀実
    • Organizer
      日本物理学会第69回年次大会
    • Place of Presentation
      神奈川
    • Related Report
      2013 Annual Research Report
  • [Presentation] 分子動力学法によるタンパク質-基質分子間の自由エネルギープロフィール2014

    • Author(s)
      川口一朋、齋藤大明、長尾秀実
    • Organizer
      日本物理学会第69回年次大会
    • Place of Presentation
      神奈川
    • Related Report
      2013 Annual Research Report
  • [Presentation] 分子動力学法によるグラミシジンAの膜内安定性2014

    • Author(s)
      齋藤 大明,川口 一朋,長尾 秀実
    • Organizer
      日本化学会第94春季年会
    • Place of Presentation
      名古屋
    • Related Report
      2013 Annual Research Report
  • [Presentation] Molecular dynamics study on mean force and free energy difference between Hsp90 and ADP2014

    • Author(s)
      Kazutomo KAWAGUCHI, Hiroaki SAITO, Hidemi NAGAO
    • Organizer
      Nagoya Symposium on Depletion Forces: Celebrating the 60th Anniversary of the Asakura-Oosawa Theory
    • Place of Presentation
      名古屋
    • Related Report
      2013 Annual Research Report
  • [Presentation] Molecular Dynamics Study of Gramicidin A in Lipid Bilayer: Electrostatic Map and Ion Conduction2013

    • Author(s)
      Hiroaki SAITO, Masashi IWAYAMA, Kazutomo KAWAGUCHI, Taku MIZUKAMI, Takeshi MIYAKAWA, Masako TAKASU, and Hidemi NAGAO
    • Organizer
      The 12th Asia Pacific Physics Conference (APPC12)
    • Place of Presentation
      千葉
    • Related Report
      2013 Annual Research Report
  • [Presentation] Molecular Dynamics Study of Hsp90 and ADP: Hydrogen Bond Analysis for ADP Dissociation2013

    • Author(s)
      Kazutomo KAWAGUCHI, Hiroaki SAITO, Hidemi NAGAO
    • Organizer
      The 12th Asia Pacific Physics Conference (APPC12)
    • Place of Presentation
      千葉
    • Related Report
      2013 Annual Research Report
  • [Presentation] Protein--protein interactions of Azurin complex in liquid system2013

    • Author(s)
      Micke Rusmerryani, Masako Takasu, Kazutomo Kawaguchi, Hiroaki Saito, and Hidemi Nagao
    • Organizer
      The 12th Asia Pacific Physics Conference (APPC12)
    • Place of Presentation
      千葉
    • Related Report
      2013 Annual Research Report
  • [Presentation] Π-stacking Interaction between Heterocyclic Rings in a Reaction Field of Biological System2013

    • Author(s)
      Muhamad KOYIMATU, Hideto SHIMAHARA, Kimikazu SUGIMORI, Kazutomo KAWAGUCHI, Hiroaki SAITO, and Hidemi NAGAO
    • Organizer
      The 12th Asia Pacific Physics Conference (APPC12)
    • Place of Presentation
      千葉
    • Related Report
      2013 Annual Research Report
  • [Presentation] MD法とQM/MM計算によるブルー銅タンパク質の酸化還元電位に関する理論的研究2013

    • Author(s)
      岩山 将士,齋藤 大明,杉森 公一,川口 一朋,長尾 秀実
    • Organizer
      第7回分子科学討論会
    • Place of Presentation
      京都
    • Related Report
      2013 Annual Research Report
  • [Presentation] Theoretical studies on effects of protein--protein interactions on azurin complex stability by coarse-grained model2013

    • Author(s)
      Rusmerryani Micke,Takasu Masako,Kawaguchi Kazutomo,Saito Hiroaki,Nagao Hidemi
    • Organizer
      第7回分子科学討論会
    • Place of Presentation
      京都
    • Related Report
      2013 Annual Research Report
  • [Presentation] Theoretical Study of a π-stacking Interaction Effect to the Orientation of His64 of Carbonic Anhydrase2013

    • Author(s)
      Koyimatu Muhamad,Shimahara Hideto,Sugimori Kimikazu,Sugimori Tetsuya,Saito Hirosaki,Kawaguchi Kazutomo,Nagao Hidemi
    • Organizer
      第7回分子科学討論会
    • Place of Presentation
      京都
    • Related Report
      2013 Annual Research Report
  • [Presentation] Structure and stability of the binding of HNP-1 with DPPC lipid bilayer: a molecular dynamics study2013

    • Author(s)
      Primasari Nandia,Saito Hiroaki,Nurbaiti Santi,Kawaguchi Kazutomo,Nagao Hidemi
    • Organizer
      第7回分子科学討論会
    • Place of Presentation
      京都
    • Related Report
      2013 Annual Research Report
  • [Presentation] Hsp90とADPの解離過程における自由エネルギープロフィールと相互作用解析2013

    • Author(s)
      川口 一朋,齋藤 大明,長尾 秀実
    • Organizer
      第7回分子科学討論会
    • Place of Presentation
      京都
    • Related Report
      2013 Annual Research Report
  • [Presentation] 脂質二重層膜におけるグラミシジンAの静電ポテンシャル特性と電場応答2013

    • Author(s)
      齋藤 大明,川口 一朋,長尾 秀実
    • Organizer
      第7回分子科学討論会
    • Place of Presentation
      京都
    • Related Report
      2013 Annual Research Report
  • [Presentation] Electrostatic potential and lateral pressure profile of lipid bilayer containing gramicidin A in effective electrostatic field2013

    • Author(s)
      齋藤 大明,川口 一朋,長尾 秀実
    • Organizer
      第51回生物物理年会
    • Place of Presentation
      京都
    • Related Report
      2013 Annual Research Report
  • [Presentation] Analysis of network of water molecules in molecular dynamics simulations of Hras-GTP and GDP complexes2013

    • Author(s)
      Takeshi Miyakawa, Ryota Morikawa, Masako Takasu, Kimikazu Sugimori, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
    • Organizer
      第51回生物物理年会
    • Place of Presentation
      京都
    • Related Report
      2013 Annual Research Report
  • [Presentation] Free energy profile and dissociation pathway in the dissociation process of ADP from Hsp902013

    • Author(s)
      Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
    • Organizer
      第51回生物物理年会
    • Place of Presentation
      京都
    • Related Report
      2013 Annual Research Report
  • [Presentation] Development of new algolithm for calculation of the energy distribution function by GPGPU2013

    • Author(s)
      Takuhito Shiogama, Tsuhito Yoshida, Hiroaki Saito, Kazutomo Kawaguchi, Hidemi Nagao
    • Organizer
      第51回生物物理年会
    • Place of Presentation
      京都
    • Related Report
      2013 Annual Research Report
  • [Presentation] Theoretical study on the structural stability of the vesicle by parallelized coarse-grained simulation2013

    • Author(s)
      Tsuhito Yoshida, Kazuma Tamura, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
    • Organizer
      第51回生物物理年会
    • Place of Presentation
      京都
    • Related Report
      2013 Annual Research Report
  • [Presentation] Theoretical study on the self-assembly of satellite tobacco mosaic virus using coarse grained simulation2013

    • Author(s)
      Masato Teranishi, Micke Rusmerryani, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
    • Organizer
      第51回生物物理年会
    • Place of Presentation
      京都
    • Related Report
      2013 Annual Research Report
  • [Presentation] Theoretical studies of redox potential for metalloprotein by combining MD and QM/MM simulations2013

    • Author(s)
      Masashi Iwayama, Hiroaki Saito, Kimikazu Sugimori, Kazutomo Kawaguchi, Hidemi Nagao
    • Organizer
      3rd International Conference on Molecular Simulatio
    • Place of Presentation
      神戸
    • Related Report
      2013 Annual Research Report
  • [Presentation] Thermal Statibilty of Gramicidin A in Lipid Bilayer: A Molecular Dynamics Study2013

    • Author(s)
      Hiroaki Saito, Kawaguchi Kazutomo, Hidemi Nagao
    • Organizer
      3rd International Conference on Molecular Simulation
    • Place of Presentation
      神戸
    • Related Report
      2013 Annual Research Report
  • [Presentation] Molecular dynamics study on mean force between Hsp90 and ADP2013

    • Author(s)
      Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
    • Organizer
      3rd International Conference on Molecular Simulation
    • Place of Presentation
      神戸
    • Related Report
      2013 Annual Research Report
  • [Presentation] Theoretical studies on oxidation of molecules by combining MD and QM/MM calculations2013

    • Author(s)
      Masashi Iwayama, Isman Kurniawan, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
    • Organizer
      The 53rd Sanibel Symposium
    • Place of Presentation
      Florida, USA
    • Related Report
      2012 Research-status Report
  • [Presentation] Hras-GTP内におけるGTP周辺にある水分子の分子動力学法による研究2013

    • Author(s)
      宮川毅, 森河良太, 高須昌子, 杉森公一, 川口一朋, 齋藤大明, 長尾秀実
    • Organizer
      第68回 日本物理学会 春季大会
    • Place of Presentation
      広島
    • Related Report
      2012 Research-status Report
  • [Presentation] Molecular dynamics study of gramicidin A in lipid bilayer: structure and lateral pressure profile2012

    • Author(s)
      Hiroaki Saito, Masashi Iwayama, Hiroyuki Takagi, Kazutomo Kawaguchi, and Hidemi Nagao
    • Organizer
      The 5th International Symposium on Computational Sciences (ISCS) 2012
    • Place of Presentation
      Yogyakarta, Indonesia
    • Related Report
      2012 Research-status Report
    • Invited
  • [Presentation] Free energy profile for binding of ADP to Hsp90 by molecular dynamics simulation2012

    • Author(s)
      Kazutomo Kawaguchi, Hiroyuki Takagi, Masashi Iwayama, Hiroaki Saito, and Hidemi Nagao
    • Organizer
      The 5th International Symposium on Computational Sciences (ISCS) 2012
    • Place of Presentation
      Yogyakarta, Indonesia
    • Related Report
      2012 Research-status Report
    • Invited
  • [Presentation] 脂質二重層膜におけるグラミシジンAの構造と圧力特性2012

    • Author(s)
      齋藤 大明,川口 一朋,長尾 秀実
    • Organizer
      第6回分子化学討論会
    • Place of Presentation
      東京
    • Related Report
      2012 Research-status Report
  • [Presentation] Dual Go-Modelを用いたジヒドロ葉酸還元酵素の構造遷移解析2012

    • Author(s)
      寺西 壯登,川口 一朋,齋藤 大明,長尾 秀実
    • Organizer
      第6回分子化学討論会
    • Place of Presentation
      東京
    • Related Report
      2012 Research-status Report
  • [Presentation] 炭酸脱水酵素の水素結合ネットワークとHis642012

    • Author(s)
      島原 秀登,杉森 公一,岩山 将士,杉森 哲也,川口 一朋,齊藤 大明,吉田 卓也,中沢 隆,大久保 忠恭,小林 祐次,長尾 秀実
    • Organizer
      第6回分子化学討論会
    • Place of Presentation
      東京
    • Related Report
      2012 Research-status Report
  • [Presentation] GPGPUによるエネルギー分布関数計算の高速化2012

    • Author(s)
      塩釜 拓仁,齋藤 大明,川口 一朋,長尾 秀実
    • Organizer
      第6回分子化学討論会
    • Place of Presentation
      東京
    • Related Report
      2012 Research-status Report
  • [Presentation] 分子動力学計算における相互作用計算の高速化手法の評価2012

    • Author(s)
      吉田 津日門,齋藤 大明,川口 一朋,長尾 秀実
    • Organizer
      第6回分子化学討論会
    • Place of Presentation
      東京
    • Related Report
      2012 Research-status Report
  • [Presentation] Free energy profile for binding of ADP to Hsp90 with molecular dynamics simulation2012

    • Author(s)
      K. Kawaguchi, H. Takagi, M. Iwayama, M. Nishimura, H. Saito, Hidemi Nagao
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋
    • Related Report
      2012 Research-status Report
  • [Presentation] Structure and lateral pressure profile of lipid bilayer containing gramicidin A by molecular dynamics simulation2012

    • Author(s)
      H. Saito, M. Iwayama, M. Nishimura, H. Takagi, K. Kawaguchi, H. Nagao
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋
    • Related Report
      2012 Research-status Report
  • [Presentation] Analysis of water molecules in molecular dynamics simulations of H-ras GTP and GDP complexes2012

    • Author(s)
      T. Miyakawa, R. Morikawa, M. Takasu, K. Sugimori, K. Kawaguchi, H. Saito, Hidemi Nagao
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋
    • Related Report
      2012 Research-status Report
  • [Presentation] Solvation free energy in protein docking process2012

    • Author(s)
      Taku Mizukami, Hiroaki Siato, Hidemi Nagao
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋
    • Related Report
      2012 Research-status Report
  • [Presentation] Binding Free Energy of Azurin–Cytochrome c551 Complex by all-atom Molecular Dynamics Simulation2012

    • Author(s)
      H. Saito, M. Iwayama, T. Mizukami, K. Kawaguchi, Hidemi Nagao
    • Organizer
      Conference on Computational Physics (CCP2012)
    • Place of Presentation
      Kobe, Japan
    • Related Report
      2012 Research-status Report
  • [Presentation] Free energy profile of Hsp90-ADP binding by molecular dynamics simulations2012

    • Author(s)
      K. Kawaguchi, H. Saito, Hidemi Nagao
    • Organizer
      Conference on Computational Physics (CCP2012)
    • Place of Presentation
      Kobe, Japan
    • Related Report
      2012 Research-status Report
  • [Presentation] Hsp90 との結合・解離における ADP の解析2012

    • Author(s)
      川口一朋, 齋藤大明, 長尾秀実
    • Organizer
      第26回分子シミュレーション討論会
    • Place of Presentation
      Kobe, Japan
    • Related Report
      2012 Research-status Report
  • [Presentation] 脂質二重層膜におけるグラミシジン A の構造と圧力特性2012

    • Author(s)
      齋藤大明, 川口一朋 , 長尾秀実
    • Organizer
      第26回分子シミュレーション討論会
    • Place of Presentation
      福岡
    • Related Report
      2012 Research-status Report
  • [Presentation] Molecular dynamics studies of Hsp90 with ADP: protein-ligand binding dynamics2012

    • Author(s)
      K. Kawaguchi, H. Takagi, M. Takasu, H. Saito, H. Nagao
    • Organizer
      The 4th International Symposium on Slow Dynamics in Complex Systems
    • Place of Presentation
      仙台
    • Related Report
      2012 Research-status Report
  • [Presentation] Theoretical Model for Assessing Properties of Local Structures in Metalloprotein2012

    • Author(s)
      M. Koyimatu, H. Shimahara, M. Iwayama, K. Sugimori, K. Kawaguchi, H. Saito, H. Nagao
    • Organizer
      The 4th International Symposium on Slow Dynamics in Complex Systems
    • Place of Presentation
      仙台
    • Related Report
      2012 Research-status Report
  • [Presentation] Oxidation Potential of Ketone Molecule: Structural Fluctuation Dependence2012

    • Author(s)
      Isman Kurniawan, Muhamad Koyimatu, Masashi Iwayama, Hiroaki Saito, Kazutomo Kawaguchi, Hidemi Nagao
    • Organizer
      The 4th International Symposium on Slow Dynamics in Complex Systems
    • Place of Presentation
      仙台
    • Related Report
      2012 Research-status Report
  • [Presentation] A molecular dynamics study of Hras-GTP and GDP complexes: the properties of water molecules around guanine nucleotide2012

    • Author(s)
      T. Miyakawa, R. Morikawa, M. Takasu, K. Sugimori, K. Kawaguchi, H. Saito, H. Nagao
    • Organizer
      The 4th International Symposium on Slow Dynamics in Complex Systems
    • Place of Presentation
      仙台
    • Related Report
      2012 Research-status Report
  • [Presentation] Conformational Stability of Met20 Loop of DHFR: A molecular Dynamics Study2012

    • Author(s)
      M. Nishimura, H. Saito, K. Kawaguchi, H. Nagao
    • Organizer
      The 4th International Symposium on Slow Dynamics in Complex Systems
    • Place of Presentation
      仙台
    • Related Report
      2012 Research-status Report
  • [Presentation] Evaluation of scoring functions for protein-ligand docking2012

    • Author(s)
      Meidy T. Pakpahan, Micke Rusmerryani, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
    • Organizer
      The 4th International Symposium on Slow Dynamics in Complex Systems
    • Place of Presentation
      仙台
    • Related Report
      2012 Research-status Report
  • [Presentation] Transition State Analysis of Azurin via Go-like Model2012

    • Author(s)
      Micke Rusmerryani, Meidy T. Pakpahan, Megumi Nishimura, Masako Takasu, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
    • Organizer
      The 4th International Symposium on Slow Dynamics in Complex Systems
    • Place of Presentation
      仙台
    • Related Report
      2012 Research-status Report
  • [Presentation] Molecular dynamics study of electrostatic potential along lipid bilayer with gramicidin A2012

    • Author(s)
      Hiroaki Saito, Megumi Nishimura, Hiroyuki Takagi, Takeshi, Miyakawa, Kazutomo Kawaguchi, Hidemi Nagao
    • Organizer
      The 4th International Symposium on Slow Dynamics in Complex Systems
    • Place of Presentation
      仙台
    • Related Report
      2012 Research-status Report
  • [Presentation] Theoretical study on entrainment phenomenon in model molecular systems2012

    • Author(s)
      Hidemi Nagao, Michke Rusmerryani, Acep Pruqon, Kazutomo Kawaguchi, Hiroaki Saito
    • Organizer
      The 4th International Symposium on Slow Dynamics in Complex Systems
    • Place of Presentation
      仙台
    • Related Report
      2012 Research-status Report
  • [Presentation] Molecular dynamics analyses of dissociation process of ADP from Hsp902012

    • Author(s)
      K. Kawaguchi, H. Takagi, M. Iwayama, H. Saito, H. Nagao
    • Organizer
      International Symposium On Computational Science 2013
    • Place of Presentation
      Kanazawa, Japan
    • Related Report
      2012 Research-status Report
    • Invited
  • [Presentation] Theoretical Study of π-stacking Interaction in Carbonic Anhydrase2012

    • Author(s)
      M. Koyimatu, H. Shimahara, K. Kawaguchi, H. Saito, and H. Nagao
    • Organizer
      International Symposium On Computational Science 2013
    • Place of Presentation
      Kanazawa, Japan
    • Related Report
      2012 Research-status Report
  • [Presentation] Binding Free Energy of Protein-Ligand by combining Docking and MD Simulation: A Comparison of Calculation Methods2012

    • Author(s)
      M. T. Pakpahan, H. Saito, K. Kawaguchi, and H. Nagao
    • Organizer
      International Symposium On Computational Science 2013
    • Place of Presentation
      Kanazawa, Japan
    • Related Report
      2012 Research-status Report
  • [Presentation] Computational Study of Oxidation Potential Fluctuation of Ketone Molecule2012

    • Author(s)
      Isman Kurniawan, H. Saito, K. Kawaguchi, H. Nagao
    • Organizer
      International Symposium On Computational Science 2013
    • Place of Presentation
      Kanazawa, Japan
    • Related Report
      2012 Research-status Report
  • [Presentation] Molecular dynamics study of gramicidin A in lipid bilayer: structure and energetics"2012

    • Author(s)
      Hiroaki Saito, Masashi Iwayama, Hiroyuki Takagi, Takeshi Miyakawa, Kazutomo Kawaguchi, Masako Takasu, and Hidemi Nagao
    • Organizer
      The 52nd Sanibel Symposium
    • Place of Presentation
      The King and prince beach & golf resort , アメリカ
    • Related Report
      2011 Research-status Report
  • [Presentation] Molecular dynamics simulaitoins of the N-terminal domain of Hsp90 with nucleotides2012

    • Author(s)
      Kazutomo Kawaguchi Massashi Iwayama, Hiroyuki Takagi, Takeshi Miyakawa, Hiroaki Saito, Masako Takasu, Hidemi Nagao
    • Organizer
      The 52nd Sanibel Symposium
    • Place of Presentation
      The King and prince beach & golf resort , アメリカ
    • Related Report
      2011 Research-status Report
  • [Presentation] Molecular dynamics simulations of the Hras-GTP complex and the Hras-GDP complex2012

    • Author(s)
      Takeshi Miyakawa, Ryota Morikawa, Msako Takasu, Kimikazu Sugimori, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
    • Organizer
      The 52nd Sanibel Symposium
    • Place of Presentation
      The King and prince beach & golf resort , アメリカ
    • Related Report
      2011 Research-status Report
  • [Presentation] Solvation effect on the protein docking process: a molecular dynamics study2012

    • Author(s)
      Taku Mizukami, Hiroaki Saito, Takeshi Miyakawa, Masashi Iwayama, Masako Takasu, Hidemi Nagao
    • Organizer
      The 52nd Sanibel Symposium
    • Place of Presentation
      The King and prince beach & golf resort , アメリカ
    • Related Report
      2011 Research-status Report
  • [Presentation] Binding free energy of oxidized Azurin - reduced Cytochrome c551 Complex2011

    • Author(s)
      Hiroaki Saito, Masashi Iwayama, Taku Mizukami, Hidemi Nagao
    • Organizer
      The Seventh Congress of the International Society for Theoretical Chemical Physics (ISTCP-VII)
    • Place of Presentation
      早稲田大学, 東京
    • Related Report
      2011 Research-status Report
  • [Presentation] Theoretical Study on the Redox Reaction of Azurin in Water Solvent2011

    • Author(s)
      Masashi Iwayama, Hiroaki Saito, Kazutomo Kawaguchi, Hidemi Nagao
    • Organizer
      XVIth International Workshop on Quantum Systems in Chemistry and Physics (QSCP-XVI)
    • Place of Presentation
      石川県立美術館, 石川県
    • Related Report
      2011 Research-status Report
  • [Presentation] Structural analysis of ligand binding mechanism of Hsp902011

    • Author(s)
      Kazutomo Kawaguchi, Acep Purqon, Hiroaki Saito, Hidemi Nagao
    • Organizer
      XVIth International Workshop on Quantum Systems in Chemistry and Physics (QSCP-XVI)
    • Place of Presentation
      石川県立美術館, 石川県
    • Related Report
      2011 Research-status Report
  • [Presentation] Free energy of cell-penetrating peptide in lipid bilayer membrane: coarse-grained simulation2011

    • Author(s)
      Shuhei Kawamoto, Takeshi Miyakawa, Masako Takasu, Ryota Morikawa, Tatsuki Oda, Hiroaki Saito, Shiroh Futaki
    • Organizer
      XVIth International Workshop on Quantum Systems in Chemistry and Physics (QSCP-XVI)
    • Place of Presentation
      石川県立美術館, 石川県
    • Related Report
      2011 Research-status Report
  • [Presentation] The potentials of the atoms around Mg2+ in the H-ras GTP complex and in the H-ras GDP complex2011

    • Author(s)
      Takeshi Miyakawa, Ryota Morikawa, Masako Takasu, Kimikazu Sugimori, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
    • Organizer
      XVIth International Workshop on Quantum Systems in Chemistry and Physics (QSCP-XVI)
    • Place of Presentation
      石川県立美術館, 石川県
    • Related Report
      2011 Research-status Report
  • [Presentation] Structure and dynamics of glutathione and glutathione-transferaseT2-2: a molecular dynamics study2011

    • Author(s)
      Yuriko Omae, Hiroaki Saito, Kazutomo Kawaguchi, Hidemi Nagao
    • Organizer
      XVIth International Workshop on Quantum Systems in Chemistry and Physics (QSCP-XVI)
    • Place of Presentation
      石川県立美術館, 石川県
    • Related Report
      2011 Research-status Report
  • [Presentation] Free energy profile of water across cholesterol containing lipid bilayer2011

    • Author(s)
      Hiroaki Saito, Wataru Shinoda
    • Organizer
      XVIth International Workshop on Quantum Systems in Chemistry and Physics (QSCP-XVI)
    • Place of Presentation
      石川県立美術館, 石川県
    • Related Report
      2011 Research-status Report
  • [Presentation] グラミシジンAを添加した脂質二重層膜の分子動力学シミュレーション2011

    • Author(s)
      齋藤大明,アチェププルコン,川口一朋,長尾秀実
    • Organizer
      第5回分子科学討論会
    • Place of Presentation
      札幌コンベンションセンター, 北海道
    • Related Report
      2011 Research-status Report
  • [Presentation] 分子動力学法によるDHFRの構造変位に対する自由エネルギー変化2011

    • Author(s)
      西村めぐみ, 齋藤大明, 川口一朋, AcepPurqon, 長尾秀実
    • Organizer
      第5回分子科学討論会
    • Place of Presentation
      札幌コンベンションセンター, 北海道
    • Related Report
      2011 Research-status Report
  • [Presentation] 分子動力学法によるHsp90と基質分子の自由エネルギー解析2011

    • Author(s)
      川口一朋、Acep Purqon、齋藤大明、長尾秀実
    • Organizer
      第5回分子科学討論会
    • Place of Presentation
      札幌コンベンションセンター, 北海道
    • Related Report
      2011 Research-status Report
  • [Presentation] ドパミン受容体-リガンド分子間の結合自由エネルギー解析2011

    • Author(s)
      高木 啓行,川口 一朋,齋藤 大明,Acep Purqon,長尾 秀実
    • Organizer
      第5回分子科学討論会
    • Place of Presentation
      札幌コンベンションセンター, 北海道
    • Related Report
      2011 Research-status Report
  • [Presentation] 溶液中における鉄イオンFe2+/Fe3+の酸化還元電位に関する理論的研究2011

    • Author(s)
      岩山将士, 齋藤大明, 川口一朋, 長尾秀実
    • Organizer
      第5回分子科学討論会
    • Place of Presentation
      札幌コンベンションセンター, 北海道
    • Related Report
      2011 Research-status Report
  • [Presentation] 分子動力学シミュレーションによるグルタチオンとグルタチオン転移酵素T2-2の結合エネルギー計算2011

    • Author(s)
      大前裕莉子,齋藤大明,川口一朋,長尾秀実
    • Organizer
      第5回分子科学討論会
    • Place of Presentation
      札幌コンベンションセンター, 北海道
    • Related Report
      2011 Research-status Report
  • [Presentation] 量子化学計算によるアスコルビン酸の酸化還元電位2011

    • Author(s)
      杉森哲也,齋藤大明,川口一朋,西川清,長尾秀実
    • Organizer
      第5回分子科学討論会
    • Place of Presentation
      札幌コンベンションセンター, 北海道
    • Related Report
      2011 Research-status Report
  • [Presentation] 膜透過ペプチドによる脂質二重膜の構造変化の膜曲げ弾性依存2011

    • Author(s)
      川本周平, 高須昌子, 宮川毅, 森河良太, 小田竜樹, 齋藤大明, 二木史朗, 長尾秀実
    • Organizer
      第49回生物物理学会年会
    • Place of Presentation
      兵庫県立大学, 兵庫県
    • Related Report
      2011 Research-status Report
  • [Presentation] H-ras GTP複合体とH-ras GDP複合体の分子動力学シミュレーション2011

    • Author(s)
      宮川毅, 森河良太, 高須昌子, 齋藤大明, 長尾秀実
    • Organizer
      第49回生物物理学会年会
    • Place of Presentation
      兵庫県立大学, 兵庫県
    • Related Report
      2011 Research-status Report
  • [Presentation] C型肝炎ウイルスにおけるNS3セリンプロテアーゼ阻害剤cVH種に関する分子動力学シミュレーション2011

    • Author(s)
      岩山将士, 川口一朋, 齋藤大明, 長尾秀実
    • Organizer
      第49回生物物理学会年会
    • Place of Presentation
      兵庫県立大学, 兵庫県
    • Related Report
      2011 Research-status Report
  • [Presentation] PYP構造変化に伴う溶媒和自由エネルギーの変化2011

    • Author(s)
      水上卓, 齋藤大明, 長尾秀実
    • Organizer
      第49回生物物理学会年会
    • Place of Presentation
      兵庫県立大学, 兵庫県
    • Related Report
      2011 Research-status Report
  • [Presentation] Azurin-Cytochrome c551 複合体の結合自由エネルギー2011

    • Author(s)
      齋藤大明, 岩山将士, 水上卓, 西川清
    • Organizer
      第2回計算統計物理学研究会
    • Place of Presentation
      金沢大学, 石川県
    • Related Report
      2011 Research-status Report
  • [Presentation] コレステロールを含んだ脂質二重膜の水分子透過性2011

    • Author(s)
      齋藤大明,篠田渉
    • Organizer
      第25回分子シミュレーション討論会
    • Place of Presentation
      東京工業大学, 東京
    • Related Report
      2011 Research-status Report
  • [Presentation] 熱力学的積分法を用いた Hsp90 と基質分子の結合自由エネルギープロフィール2011

    • Author(s)
      川口一朋,A. Purqon,齋藤大明,長尾秀実
    • Organizer
      第25回分子シミュレーション討論会
    • Place of Presentation
      東京工業大学, 東京
    • Related Report
      2011 Research-status Report
  • [Presentation] Hras-GTP 結合系ならびに Hras-GDP 結合系の分子動力学シミュレーション2011

    • Author(s)
      宮川毅,森河良太,高須昌子,杉森公一, 川口一朋,齋藤大明,長尾秀実
    • Organizer
      第25回分子シミュレーション討論会
    • Place of Presentation
      東京工業大学, 東京
    • Related Report
      2011 Research-status Report
  • [Presentation] 膜透過ペプチドの脂質二重膜内における自由エネルギー2011

    • Author(s)
      川本周平,高須昌子,宮川毅,森河良太,小田竜樹,齋藤大明,二木史朗,長尾秀実
    • Organizer
      第25回分子シミュレーション討論会
    • Place of Presentation
      東京工業大学, 東京
    • Related Report
      2011 Research-status Report

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Published: 2011-08-05   Modified: 2019-07-29  

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