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1

Analysis of water molecules around GTP in Hras-GTP complex and GDP in Hras-GDP complex by molecular dynamics simulations

Miyakawa, Takeshi, Morikawa, Ryota, Takasu, Masako, Sugimori, Kimikazu, Kawaguchi, Kazutomo, Saito, Hiroaki, Nagao, Hidemi

Journal:

Molecular Physics

Year:

2014

Language:

english

File:

PDF, 592 KB

english, 2014

2

1P057 Theoretical study on the self-assembly of satellite tobacco mosaic virus using coarse grained simulation(01C. Protein:Property,Poster)

Teranishi, Masato, Rusmerryani, Micke, Kawaguchi, Kazutomo, Saito, Hiroaki, Nagao, Hidemi

Journal:

Seibutsu Butsuri

Year:

2013

Language:

english

File:

PDF, 693 KB

english, 2013

3

The Study of the Octanol-Water Partition Coefficient by the Computational Chemistry Method; è¨ç®åå¦çææ³ã«ããæ°´/ãªã¯ã¿ãã¼ã«åéä¿æ°ã®ç ç©¶;

KODAMA, Koichi, SYAH, Arwan, KAWAGUCHI, Kazutomo, MATSUI, Toru, NAGAO, Hidemi, SHIGETA, Yasuteru

Journal:

Journal of Computer Chemistry Japan

Year:

2019

File:

PDF, 917 KB

2019

4

Theoretical prediction of optical absorption maxima for photosensory receptor mutants

Kazutomo Kawaguchi, Takahisa Yamato

Journal:

Chemical Physics Letters

Year:

2006

Language:

english

File:

PDF, 404 KB

english, 2006

5

Molecular dynamics study of gramicidin a in lipid bilayer: Structure and lateral pressure profile

Hiroaki Saito, Masashi Iwayama, Hiroyuki Takagi, Megumi Nishimura, Takeshi Miyakawa, Kazutomo Kawaguchi, Masako Takasu, Taku Mizukami, Hidemi Nagao

Journal:

International Journal of Quantum Chemistry

Year:

2012

Language:

english

File:

PDF, 452 KB

english, 2012

6

Molecular dynamics analyses of the dissociation process of ADP from Hsp90

Kazutomo Kawaguchi, Hiroyuki Takagi, Masashi Iwayama, Megumi Nishimura, Takeshi Miyakawa, Hiroaki Saito, Masako Takasu, Hidemi Nagao

Journal:

International Journal of Quantum Chemistry

Year:

2012

Language:

english

File:

PDF, 459 KB

english, 2012

7

MODYLAS: A Highly Parallelized General-Purpose Molecular Dynamics Simulation Program for Large-Scale Systems with Long-Range Forces Calculated by Fast Multipole Method (FMM) and Highly Scalable Fine-Grained New Parallel Processing Algorithms

Andoh, Yoshimichi, Yoshii, Noriyuki, Fujimoto, Kazushi, Mizutani, Keisuke, Kojima, Hidekazu, Yamada, Atsushi, Okazaki, Susumu, Kawaguchi, Kazutomo, Nagao, Hidemi, Iwahashi, Kensuke, Mizutani, Fumiyasu

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 598 KB

english, 2013

8

Molecular dynamics simulations of the Hras-GTP complex and the Hras-GDP complex

Miyakawa, Takeshi, Morikawa, Ryota, Takasu, Masako, Sugimori, Kimikazu, Mizukami, Taku, Kawaguchi, Kazutomo, Saito, Hiroaki, Nagao, Hidemi

Journal:

International Journal of Quantum Chemistry

Year:

2013

Language:

english

File:

PDF, 353 KB

english, 2013

9

Molecular dynamics study on the free energy profile for dissociation of ADP from N-terminal domain of Hsp90

Kawaguchi, Kazutomo, Saito, Hiroaki, Okazaki, Susumu, Nagao, Hidemi

Journal:

Chemical Physics Letters

Year:

2013

Language:

english

File:

PDF, 1.07 MB

english, 2013

10

Effect of zinc on liver cirrhosis with hyperammonemia: A preliminary randomized, placebo-controlled double-blind trial

Katayama, Kazuhiro, Saito, Masanori, Kawaguchi, Takumi, Endo, Ryujin, Sawara, Kei, Nishiguchi, Shuhei, Kato, Akinobu, Kohgo, Hiroshi, Suzuki, Kazutomo, Sakaida, Isao, Ueno, Yoshiyuki, Habu, Daiki, Ito

Journal:

Year:

2014

Language:

english

File:

PDF, 203 KB

english, 2014

11

Branched-Chain Amino Acids Prevent Hepatocarcinogenesis and Prolong Survival of Patients With Cirrhosis

Kawaguchi, Takumi, Shiraishi, Koichi, Ito, Toshifumi, Suzuki, Kazutomo, Koreeda, Chizu, Ohtake, Takaaki, Iwasa, Motoh, Tokumoto, Yoshio, Endo, Ryujin, Kawamura, Nao–hiro, Shiraki, Makoto, Habu, Daiki,

Journal:

Clinical Gastroenterology and Hepatology

Year:

2014

Language:

english

File:

PDF, 494 KB

english, 2014

12

Membership Application

Koike, Kana, Kawaguchi, Kazutomo, Yamato, Takahisa

Journal:

Antennas and Propagation Newsletter, IEEE Professional Group on

Year:

2004

Language:

english

File:

PDF, 76 KB

english, 2004

13

A hybrid-type approach with MD and DFT calculations for evaluation of redox potential of molecules

Iwayama, Masashi, Kurniawan, Isman, Kawaguchi, Kazutomo, Saito, Hiroaki, Nagao, Hidemi

Journal:

Molecular Simulation

Year:

2015

Language:

english

File:

PDF, 161 KB

english, 2015

14

AIP Conference Proceedings [AIP Publishing LLC TIMES OF POLYMERS (TOP) AND COMPOSITES 2014: Proceedings of the 7th International Conference on Times of Polymers (TOP) and Composites - Ischia, Italy (22–26 June 2014)] - Solvent site-dipole fields around guanine nucleotides in the Hras-GTP complex and in the Hras-GDP complex

Miyakawa, Takeshi, Morikawa, Ryota, Takasu, Masako, Sugimori, Kimikazu, Kawaguchi, Kazutomo, Saito, Hiroaki, Nagao, Hidemi

Year:

2014

Language:

english

File:

PDF, 229 KB

english, 2014

15

[Journal of the Physical Society of Japan Proceedings of the 12th Asia Pacific Physics Conference (APPC12) - Makuhari, Japan (July 14–19, 2013)] Proceedings of the 12th Asia Pacific Physics Conference (APPC12) - Protein–Protein Interactions of Azurin Complex by Coarse-Grained Simulations with a Gō-Like Model

Rusmerryani, Micke, Takasu, Masako, Kawaguchi, Kazutomo, Saito, Hiroaki, Nagao, Hidemi

Year:

2014

Language:

english

File:

PDF, 513 KB

english, 2014

16

[Journal of the Physical Society of Japan Proceedings of the 12th Asia Pacific Physics Conference (APPC12) - Makuhari, Japan (July 14–19, 2013)] Proceedings of the 12th Asia Pacific Physics Conference (APPC12) - Molecular Dynamics Study of Gramicidin A in Lipid Bilayer: Electrostatic Map and Ion Conduction

Saito, Hiroaki, Iwayama, Masashi, Kawaguchi, Kazutomo, Mizukami, Taku, Miyakawa, Takeshi, Takasu, Masako, Nagao, Hidemi

Year:

2014

Language:

english

File:

PDF, 798 KB

english, 2014

17

Decomposition analysis of free energy profile for Hsp90-ADP association

Kawaguchi, Kazutomo, Saito, Hiroaki, Nagao, Hidemi

Journal:

Molecular Simulation

Year:

2015

Language:

english

File:

PDF, 854 KB

english, 2015

18

AIP Conference Proceedings [American Institute of Physics 4TH INTERNATIONAL SYMPOSIUM ON SLOW DYNAMICS IN COMPLEX SYSTEMS: Keep Going Tohoku - Sendai, Japan (2–7 December 2012)] - Molecular dynamics study on entrainment phenomenon in model molecular systems

Nagao, Hidemi, Kawamoto, Shuhei, Rusmerryani, Micke, Purqon, Acep, Kawaguchi, Kazutomo, Saito, Hiroaki

Year:

2013

Language:

english

File:

PDF, 1.02 MB

english, 2013

19

AIP Conference Proceedings [American Institute of Physics 4TH INTERNATIONAL SYMPOSIUM ON SLOW DYNAMICS IN COMPLEX SYSTEMS: Keep Going Tohoku - Sendai, Japan (2–7 December 2012)] - Molecular dynamics studies of Hsp90 with ADP: Protein-ligand binding dynamics

Kawaguchi, Kazutomo, Takagi, Hiroyuki, Takasu, Masako, Saito, Hiroaki, Nagao, Hidemi

Year:

2013

Language:

english

File:

PDF, 987 KB

english, 2013

20

AIP Conference Proceedings [American Institute of Physics 4TH INTERNATIONAL SYMPOSIUM ON SLOW DYNAMICS IN COMPLEX SYSTEMS: Keep Going Tohoku - Sendai, Japan (2–7 December 2012)] - Conformational stability of Met20 loop of DHFR: A molecular dynamics study

Nishimura, Megumi, Saito, Hiroaki, Kawaguchi, Kazutomo, Nagao, Hidemi

Year:

2013

Language:

english

File:

PDF, 352 KB

english, 2013

21

A simple coarse-grained model for interacting protein complex

Kawaguchi, Kazutomo, Nakagawa, Satoshi, Kinoshita, Shogo, Wada, Makoto, Saito, Hiroaki, Nagao, Hidemi

Journal:

Molecular Physics

Year:

2017

Language:

english

File:

PDF, 1008 KB

english, 2017

22

AIP Conference Proceedings [American Institute of Physics 4TH INTERNATIONAL SYMPOSIUM ON SLOW DYNAMICS IN COMPLEX SYSTEMS: Keep Going Tohoku - Sendai, Japan (2–7 December 2012)] - Molecular dynamics study of electrostatic potential along lipid bilayer with gramicidin A

Saito, Hiroaki, Nishimura, Megumi, Takagi, Hiroyuki, Miyakawa, Takeshi, Kawaguchi, Kazutomo, Nagao, Hidemi

Year:

2013

Language:

english

File:

PDF, 1.14 MB

english, 2013

23

Theoretical study on interaction of cytochrome f and plastocyanin complex by a simple coarse-grained model with molecular crowding effect

Nakagawa, Satoshi, Kurniawan, Isman, Kodama, Koichi, Arwansyah, Muhammad Saleh, Kawaguchi, Kazutomo, Nagao, Hidemi

Journal:

Molecular Physics

Year:

2017

Language:

english

File:

PDF, 1.23 MB

english, 2017

24

A coarse-grained model of the effective interaction for charged amino acid residues and its application to formation of GCN4-pLI tetramer

Kawaguchi, Kazutomo, Nakagawa, Satoshi, Kurniawan, Isman, Kodama, Koichi, Arwansyah, Muhammad Saleh, Nagao, Hidemi

Journal:

Molecular Physics

Year:

2017

Language:

english

File:

PDF, 1.33 MB

english, 2017

25

3G1112 Molecular Dynamics Simulations of cVH domain antibody inhibitor of HCV NS3 protease(3G Protein: Structure 3,The 49th Annual Meeting of the Biophysical Society of Japan)

Iwayama, Masashi, Kawaguchi, Kazutomo, Saito, Hiroaki, Nagao, Hidemi

Journal:

Seibutsu Butsuri

Year:

2011

Language:

english

File:

PDF, 255 KB

english, 2011

26

1C1424 Molecular dynamics simulations of the N-terminal domain of Hsp90 with ligand molecules(Nucleic acid,The 49th Annual Meeting of the Biophysical Society of Japan)

Kawaguchi, Kazutomo, Nagao, Hidemi

Journal:

Seibutsu Butsuri

Year:

2011

Language:

english

File:

PDF, 221 KB

english, 2011

27

3F1010 Structure and lateral pressure profile of lipid bilayer containing gramicidin A by molecular dynamics simulation(Membrane Proteins,Oral Presentation)

Saito, Hiroaki, Iwayama, Masashi, Nishimura, Megumi, Takagi, Hiroyuki, Kawaguchi, Kazutomo, Nagao, Hidemi

Journal:

Seibutsu Butsuri

Year:

2012

Language:

english

File:

PDF, 214 KB

english, 2012

28

2P019 Analysis of network of water molecules in molecular dynamics simulations of Hras-GTP and GDP complexes(01A. Protein: Structure,Poster)

Miyakawa, Takeshi, Morikawa, Ryota, Takasu, Masako, Sugimori, Kimikazu, Kawaguchi, Kazutomo, Saito, Hiroaki, Nagao, Hidemi

Journal:

Seibutsu Butsuri

Year:

2013

Language:

english

File:

PDF, 692 KB

english, 2013

29

1E1400 Free energy profile for binding of ADP to Hsp90 with molecular dynamics simulation(Proteins: Property I,Oral Presentation,The 50th Annual Meeting of the Biophysical Society of Japan)

Kawaguchi, Kazutomo, Takagi, Hiroyuki, Iwayama, Masashi, Nishimura, Megumi, Saito, Hiroaki, Nagao, Hidemi

Journal:

Seibutsu Butsuri

Year:

2012

Language:

english

File:

PDF, 216 KB

english, 2012

30

3P206 Theoretical study on the structural stability of the vesicle by parallelized coarse-grained simulation(13A. Biological & Artifical membrane: Structure & Property,Poster)

Yoshida, Tsuhito, Tamura, Kazuma, Kawaguchi, Kazutomo, Saito, Hiroaki, Nagao, Hidemi

Journal:

Seibutsu Butsuri

Year:

2013

Language:

english

File:

PDF, 693 KB

english, 2013

31

3P008 Analysis of hydrogen bonds between solvent water and atoms in the Hras-GTP complex by molecular dynamics simulations(01A. Protein: Structure,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Takeshi, Miyakawa, Morikawa, Ryota, Takasu, Masako, Sugimori, Kimikazu, Kawaguchi, Kazutomo, Saito, Hiroaki, Nagao, Hidemi

Journal:

Seibutsu Butsuri

Year:

2014

Language:

english

File:

PDF, 695 KB

english, 2014

32

1P415 Spectral tuning mechanism and theoretical prediction of absorption maximum of photoactive yellow protein(17. Light driven system,Poster Session,Abstract,Meeting Program of EABS &BSJ 2006)

Kawaguchi, Kazutomo, Yamato, Takahisa

Journal:

Seibutsu Butsuri

Year:

2006

Language:

english

File:

PDF, 148 KB

english, 2006

33

2PT131 Analysis of water molecules in molecular dynamics simulations of H-ras GTP and GDP complexes(The 50th Annual Meeting of the Biophysical Society of Japan)

Miyakawa, Takeshi, Morikawa, Ryota, Takasu, Masako, Sugimori, Kimikazu, Kawaguchi, Kazutomo, Saito, Hiroaki, Nagao, Hidemi

Journal:

Seibutsu Butsuri

Year:

2012

Language:

english

File:

PDF, 217 KB

english, 2012

34

2P024 Theoretical study of distribution of ADP in binding pocket of Hsp90(01B. Protein: Structure & Function,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Kawaguchi, Kazutomo, Saito, Hiroaki, Nagao, Hidemi

Journal:

Seibutsu Butsuri

Year:

2014

Language:

english

File:

PDF, 729 KB

english, 2014

35

3P249 The excited electronic state of solvated photoreceptor protein investigated by the improved MLSCMO method.(Photobiology- vision and photoreception. Actinobiology,Oral Presentations)

Kawaguchi, Kazutomo, Yamato, Takahisa

Journal:

Seibutsu Butsuri

Year:

2007

Language:

english

File:

PDF, 206 KB

english, 2007

36

3P042 Free energy profile and dissociation pathway in the dissociation process of ADP from Hsp90(01A. Protein: Structure,Poster)

Kawaguchi, Kazutomo, Saito, Hiroaki, Nagao, Hidemi

Journal:

Seibutsu Butsuri

Year:

2013

Language:

english

File:

PDF, 728 KB

english, 2013

37

3P126 Development of new algolithm for calculation of the energy distribution function by GPGPU(07. Water & Hydration & Electrolyte,Poster)

Shiogama, Takuhito, Yoshida, Tsuhito, Saito, Hiroaki, Kawaguchi, Kazutomo, Nagao, Hidemi

Journal:

Seibutsu Butsuri

Year:

2013

Language:

english

File:

PDF, 693 KB

english, 2013

38

1P012 Molecular docking study of structure and binding energy of ligand-protein complex in dissociation process(Protein: Structure,Poster,The 52th Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Hiroaki, Saito, Kazutomo, Kawaguchi, Hidemi, Nagao

Journal:

Seibutsu Butsuri

Year:

2014

Language:

english

File:

PDF, 1.04 MB

english, 2014

39

1P223 Electrostatic potential and lateral pressure profile of lipid bilayer containing gramicidin A in effective electrostatic field(13C. Biological & Artifical membrane: Excitation & Channels,Poster)

Saito, Hiroaki, Kawaguchi, Kazutomo, Nagao, Hidemi

Journal:

Seibutsu Butsuri

Year:

2013

Language:

english

File:

PDF, 693 KB

english, 2013

40

[Journal of the Physical Society of Japan Proceedings of the 12th Asia Pacific Physics Conference (APPC12) - Makuhari, Japan (July 14–19, 2013)] Proceedings of the 12th Asia Pacific Physics Conference (APPC12) - Π-Stacking Interaction between Heterocyclic Rings in a Reaction Field of Biological System

Koyimatu, Muhamad, Shimahara, Hideto, Sugimori, Kimikazu, Kawaguchi, Kazutomo, Saito, Hiroaki, Nagao, Hidemi

Language:

english

File:

PDF, 591 KB

english

41

A Theoretical Study on Redox Potential and p K a of [2Fe-2S] Cluster Model from Iron-Sulfur Proteins

Kurniawan, Isman, Kawaguchi, Kazutomo, Shoji, Mitsuo, Matsui, Toru, Shigeta, Yasuteru, Nagao, Hidemi

Journal:

Bulletin of the Chemical Society of Japan

Year:

2018

Language:

english

File:

PDF, 1.53 MB

english, 2018

42

Quantum Chemical Study of Axial Ligand Effect on the Electronic Properties of Type I Copper Protein

Kurniawan, Isman, Kawaguchi, Kazutomo, Sugimori, Kimikazu, Sakurai, Takeshi, Nagao, Hidemi

Journal:

Chemistry Letters

Year:

2018

Language:

english

File:

PDF, 1.88 MB

english, 2018

43

Theoretical study of conformational transition of CDK4 by association of cyclin D3

Kawaguchi, Kazutomo, Arwansyah, Muhammad Saleh, Kataoka, Tatsuki, Nagao, Hidemi

Journal:

Molecular Physics

Year:

2019

Language:

english

File:

PDF, 1.56 MB

english, 2019

44

Theoretical studies on association/dissociation process of plastocyanin and cytochrome f in photosynthesis

Kurniawan, Isman, Matsui, Takahiro, Nakagawa, Satoshi, Kawaguchi, Kazutomo, Nagao, Hidemi

Journal:

Journal of Physics Conference Series

Year:

2018

File:

PDF, 1.23 MB

2018

45

Hypozincemia is associated with human hepatocarcinogenesis in hepatitis C virus-related liver cirrhosis

Shigefuku, Ryuta, Iwasa, Motoh, Katayama, Kazuhiro, Eguchi, Akiko, Kawaguchi, Takumi, Shiraishi, Koichi, Ito, Toshifumi, Suzuki, Kazutomo, Koreeda, Chizu, Ohtake, Takaaki, Tokumoto, Yoshio, Endo, Ryuj

Journal:

Hepatology Research

Year:

2019

Language:

english

File:

PDF, 655 KB

english, 2019

46

[Journal of the Physical Society of Japan Proceedings of the 12th Asia Pacific Physics Conference (APPC12) - Makuhari, Japan (July 14–19, 2013)] Proceedings of the 12th Asia Pacific Physics Conference (APPC12) - Molecular Dynamics Study of Hsp90 and ADP: Hydrogen Bond Analysis for ADP Dissociation

Kawaguchi, Kazutomo, Saito, Hiroaki, Nagao, Hidemi

Language:

english

File:

PDF, 576 KB

english

47

Free energy profiles of lipid translocation across pure POPC and POPC/CHOL bilayer: all-atom molecular dynamics study

Saito, Hiroaki, Morishita, Tetsuya, Mizukami, Taku, Nishiyama, Ken-ichi, Kawaguchi, Kazutomo, Nagao, Hidemi

Journal:

Journal of Physics Conference Series

Year:

2019

File:

PDF, 670 KB

2019

48

Conformation of ultra-long-chain fatty acid in lipid bilayer: Molecular dynamics study

Kawaguchi, Kazutomo, Nakagawa, Koh M., Nakagawa, Satoshi, Shindou, Hideo, Nagao, Hidemi, Noguchi, Hiroshi

Journal:

The Journal of Chemical Physics

Year:

2020

File:

PDF, 3.69 MB

2020

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