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1

Force field parameters for rotation around χ torsion axis in nucleic acids

Hirotaka Ode, Yuri Matsuo, Saburo Neya, Tyuji Hoshino

Journal:

Journal of Computational Chemistry

Year:

2008

Language:

english

File:

PDF, 1.44 MB

english, 2008

2

Magnetic and Infrared Properties of the Azide Complex of (2,7,12,17-Tetrapropylporphycenato)iron(III): A Novel Admixing Mechanism of the S = 5/2 and S = 3/2 States

Saburo Neya, Akihiro Takahashi, Hirotaka Ode, Tyuji Hoshino, Masayuki Hata, Akira Ikezaki, Yoshiki Ohgo, Masashi Takahashi, Hirotsugu Hiramatsu, Teizo Kitagawa, Yuji Furutani, Hideki Kandori, Noriaki

Journal:

European Journal of Inorganic Chemistry

Year:

2007

Language:

english

File:

PDF, 147 KB

english, 2007

3

Implementation of π-π interactions in molecular dynamics simulation

Hitomi Yuki, Yoshikazu Tanaka, Masayuki Hata, Hidenori Ishikawa, Saburo Neya, Tyuji Hoshino

Journal:

Journal of Computational Chemistry

Year:

2007

Language:

english

File:

PDF, 413 KB

english, 2007

4

Ab initio protein structure prediction with force field parameters derived from water-phase quantum chemical calculation

Daisuke Katagiri, Hideyoshi Fuji, Saburo Neya, Tyuji Hoshino

Journal:

Journal of Computational Chemistry

Year:

2008

Language:

english

File:

PDF, 680 KB

english, 2008

5

Mechanism of the decrease in catalytic activity of human cytochrome P450 2C9 polymorphic variants investigated by computational analysis

Eri Sano, Weihua Li, Hitomi Yuki, Xinli Liu, Tomomi Furihata, Kaoru Kobayashi, Kan Chiba, Saburo Neya, Tyuji Hoshino

Journal:

Journal of Computational Chemistry

Year:

2010

Language:

english

File:

PDF, 539 KB

english, 2010

6

An epoxidation mechanism of carbamazepine by CYP3A4

Masayuki Hata, Yoshikazu Tanaka, Naoko Kyoda, Taisuke Osakabe, Hitomi Yuki, Itsuko Ishii, Mitsukazu Kitada, Saburo Neya, Tyuji Hoshino

Journal:

Bioorganic & Medicinal Chemistry

Year:

2008

Language:

english

File:

PDF, 2.37 MB

english, 2008

7

Structural and biochemical study on the inhibitory activity of derivatives of 5-nitro-furan-2-carboxylic acid for RNase H function of HIV-1 reverse transcriptase

Hiroshi Yanagita, Emiko Urano, Kishow Matsumoto, Reiko Ichikawa, Yoshihisa Takaesu, Masakazu Ogata, Tsutomu Murakami, Hongui Wu, Joe Chiba, Jun Komano, Tyuji Hoshino

Journal:

Bioorganic & Medicinal Chemistry

Year:

2011

Language:

english

File:

PDF, 1.66 MB

english, 2011

8

The morphology of GM1x/SM0.6−x/Chol0.4 planar bilayers supported on SiO2 surfaces

Yanli Mao, Ryugo Tero, Yosuke Imai, Tyuji Hoshino, Tsuneo Urisu

Journal:

Chemical Physics Letters

Year:

2008

Language:

english

File:

PDF, 1.25 MB

english, 2008

9

Clustering effects of GM1 and formation mechanisms of interdigitated liquid disordered domains in GM1/SM/CHOL-supported planar bilayers on mica surfaces

Zhiguo Shang, Yanli Mao, Ryugo Tero, Xinli Liu, Tyuji Hoshino, Motohiko Tanaka, Tsuneo Urisu

Journal:

Chemical Physics Letters

Year:

2010

Language:

english

File:

PDF, 1.22 MB

english, 2010

10

Molecular modeling of human cytochrome P450 2W1 and its interactions with substrates

Weihua Li, Yun Tang, Tyuji Hoshino, Saburo Neya

Journal:

Journal of Molecular Graphics and Modelling

Year:

2009

Language:

english

File:

PDF, 532 KB

english, 2009

11

Computational analysis of water residence on ceramide and sphingomyelin bilayer membranes

Yosuke Imai, Xinli Liu, Junya Yamagishi, Kenichi Mori, Saburo Neya, Tyuji Hoshino

Journal:

Journal of Molecular Graphics and Modelling

Year:

2010

Language:

english

File:

PDF, 803 KB

english, 2010

12

Convenient synthesis of porphine from β-tetra(tert-butyl)porphyrin

Saburo Neya, Jingshun Quan, Tyuji Hoshino, Masayuki Hata, Noriaki Funasaki

Journal:

Tetrahedron Letters

Year:

2004

Language:

english

File:

PDF, 244 KB

english, 2004

13

A novel and efficient synthesis of porphine

Saburo Neya, Jingshun Quan, Masayuki Hata, Tyuji Hoshino, Noriaki Funasaki

Journal:

Tetrahedron Letters

Year:

2006

Language:

english

File:

PDF, 99 KB

english, 2006

14

A concise synthesis of monoazaporphyrin from 1,19-dideoxybiladiene-ac

Saburo Neya, Takuya Sato, Tyuji Hoshino

Journal:

Tetrahedron Letters

Year:

2008

Language:

english

File:

PDF, 95 KB

english, 2008

15

Theoretical study on monooxygenation mechanism by cytochrome P450: an ultimate species in the substrate oxidation process

Masayuki Hata, Yoshinori Hirano, Tyuji Hoshino, Rie Nishida, Minoru Tsuda

Journal:

Journal of Molecular Structure: THEOCHEM

Year:

2005

Language:

english

File:

PDF, 136 KB

english, 2005

16

Quantum chemical study on the deacylation step of human chymase

Yoshinori Hirano, Naoki Shinmoto, Masayuki Hata, Minoru Tsuda, Tyuji Hoshino

Journal:

Journal of Molecular Structure: THEOCHEM

Year:

2005

Language:

english

File:

PDF, 553 KB

english, 2005

17

Behavior of water molecules in ATPase pocket of myosin

Kazunori Yamanaka, Noriaki Okimoto, Saburo Neya, Masayuki Hata, Tyuji Hoshino

Journal:

Journal of Molecular Structure: THEOCHEM

Year:

2006

Language:

english

File:

PDF, 1.38 MB

english, 2006

18

Theoretical analysis of the stability of helices

Takahiro Tsuchiya, Daisuke Katagiri, Masayuki Hata, Tyuji Hoshino, Minoru Tsuda

Journal:

Journal of Molecular Structure: THEOCHEM

Year:

2002

Language:

english

File:

PDF, 431 KB

english, 2002

19

Exploring coumarin egress channels in human cytochrome p450 2a6 by random acceleration and steered molecular dynamics simulations

Weihua Li, Jie Shen, Guixia Liu, Yun Tang, Tyuji Hoshino

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2011

Language:

english

File:

PDF, 588 KB

english, 2011

20

Novel Controlling Mechanism of the Oxygen Affinity in Myoglobin With Isomeric Porphyrins

Saburo Neya, Masaaki Suzuki, Tyuji Hoshino

Journal:

Artificial Organs

Year:

2009

Language:

english

File:

PDF, 277 KB

english, 2009

21

Prediction of sites of metabolism in a substrate molecule, instanced by carbamazepine oxidation by CYP3A4

Hitomi Yuki, Teruki Honma, Masayuki Hata, Tyuji Hoshino

Journal:

Bioorganic & Medicinal Chemistry

Year:

2012

Language:

english

File:

PDF, 1.27 MB

english, 2012

22

Fabrications of potential imaging probes based on a β-alkyl substituted porphyrin with a terpyridine external coordination site

Masaaki Suzuki, Tomoya Uehara, Yasushi Arano, Tyuji Hoshino, Saburo Neya

Journal:

Tetrahedron Letters

Year:

2011

Language:

english

File:

PDF, 444 KB

english, 2011

23

Surface-induced phase separation of a sphingomyelin/cholesterol/ganglioside GM1-planar bilayer on mica surfaces and microdomain molecular conformation that accelerates Aβ oligomerization

Yanli Mao, Zhiguo Shang, Yosuke Imai, Tyuji Hoshino, Ryugo Tero, Motohiko Tanaka, Naoki Yamamoto, Katsuhiko Yanagisawa, Tsuneo Urisu

Journal:

Biochimica et Biophysica Acta (BBA) - Biomembranes

Year:

2010

Language:

english

File:

PDF, 2.34 MB

english, 2010

24

Computational Characterization of Structural Role of the Non-active Site Mutation M36I of Human Immunodeficiency Virus Type 1 Protease

Hirotaka Ode, Shou Matsuyama, Masayuki Hata, Saburo Neya, Junko Kakizawa, Wataru Sugiura, Tyuji Hoshino

Journal:

Journal of Molecular Biology

Year:

2007

Language:

english

File:

PDF, 1.23 MB

english, 2007

25

A Study on the Mechanism of the Proton Transport in Bacteriorhodopsin: The Importance of the Water Molecule

Murata, Katsumi, Fujii, Yasuyuki, Enomoto, Nobuyuki, Hata, Masayuki, Hoshino, Tyuji, Tsuda, Minoru

Journal:

Biophysical Journal

Year:

2000

Language:

english

File:

PDF, 256 KB

english, 2000

26

Theoretical Studies of the ATP Hydrolysis Mechanism of Myosin

Okimoto, Noriaki, Yamanaka, Kazunori, Ueno, Junko, Hata, Masayuki, Hoshino, Tyuji, Tsuda, Minoru

Journal:

Biophysical Journal

Year:

2001

Language:

english

File:

PDF, 665 KB

english, 2001

27

Computational Studies on Prion Proteins: Effect of Ala117→Val Mutation

Okimoto, Noriaki, Yamanaka, Kazunori, Suenaga, Atsushi, Hata, Masayuki, Hoshino, Tyuji

Journal:

Biophysical Journal

Year:

2002

Language:

english

File:

PDF, 1.33 MB

english, 2002

28

Ab Initio Study of the Role of Lysine 16 for the Molecular Switching Mechanism of Ras Protein p21

Futatsugi, Noriyuki, Hata, Masayuki, Hoshino, Tyuji, Tsuda, Minoru

Journal:

Biophysical Journal

Year:

1999

Language:

english

File:

PDF, 340 KB

english, 1999

29

Formation of GM1 Ganglioside Clusters on the Lipid Membrane Containing Sphingomyeline and Cholesterol

Mori, Kenichi, Mahmood, Md. Iqbal, Neya, Saburo, Matsuzaki, Katsumi, Hoshino, Tyuji

Journal:

Journal of Physical Chemistry B

Year:

2012

Language:

english

File:

PDF, 4.51 MB

english, 2012

30

Quantum Chemical Study on the Catalytic Mechanism of the C-Subunit of cAMP-Dependent Protein Kinase

Hirano, Yoshinori, Hata, Masayuki, Hoshino, Tyuji, Tsuda, Minoru

Journal:

Journal of Physical Chemistry B

Year:

2002

Language:

english

File:

PDF, 221 KB

english, 2002

31

Binding and Aggregation Mechanism of Amyloid β-Peptides onto the GM1 Ganglioside-Containing Lipid Membrane

Hoshino, Tyuji, Mahmood, Md. Iqbal, Mori, Kenichi, Matsuzaki, Katsumi

Journal:

Journal of Physical Chemistry B

Year:

2013

Language:

english

File:

PDF, 1.92 MB

english, 2013

32

Relaxation Analysis of Ligand Binding to the Myoglobin Reconstituted with Cobaltic Heme

Neya, Saburo, Suzuki, Masaaki, Hoshino, Tyuji, Kawaguchi, Akira T.

Journal:

Inorganic Chemistry

Year:

2013

Language:

english

File:

PDF, 686 KB

english, 2013

33

Derivatives of 5-Nitro-furan-2-carboxylic Acid Carbamoylmethyl Ester Inhibit RNase H Activity Associated with HIV-1 Reverse Transcriptase

Fuji, Hideyoshi, Urano, Emiko, Futahashi, Yuko, Hamatake, Makiko, Tatsumi, Junko, Hoshino, Tyuji, Morikawa, Yuko, Yamamoto, Naoki, Komano, Jun

Journal:

Journal of Medicinal Chemistry

Year:

2009

Language:

english

File:

PDF, 1000 KB

english, 2009

34

Theoretical Study on Compound I Formation in Monooxygenation Mechanism by Cytochrome P450

Hata, Masayuki, Hirano, Yoshinori, Hoshino, Tyuji, Nishida, Rie, Tsuda, Minoru

Journal:

Journal of Physical Chemistry B

Year:

2004

Language:

english

File:

PDF, 258 KB

english, 2004

35

Skeletal Recombination Reaction of N -Fused Pentaphyrin(1.1.1.1.1) via Bromination

Suzuki, Masaaki, Hoshino, Tyuji, Neya, Saburo

Journal:

Organic Letters

Year:

2014

Language:

english

File:

PDF, 1003 KB

english, 2014

36

Monooxygenation Mechanism by Cytochrome P-450

Hata, Masayuki, Hirano, Yoshinori, Hoshino, Tyuji, Tsuda, Minoru

Journal:

Journal of the American Chemical Society

Year:

2001

Language:

english

File:

PDF, 111 KB

english, 2001

37

Computational and statistical study on the molecular interaction between antigen and antibody

Osajima, Tomonori, Suzuki, Masaaki, Neya, Saburo, Hoshino, Tyuji

Journal:

Journal of Molecular Graphics and Modelling

Year:

2014

Language:

english

File:

PDF, 4.24 MB

english, 2014

38

Hydrolysis Mechanism of the Phenylalanine−Proline Peptide Bond Specific to HIV-1 Protease: Investigation by the ab Initio Molecular Orbital Method

Okimoto, Noriaki, Tsukui, Toshiyuki, Hata, Masayuki, Hoshino, Tyuji, Tsuda, Minoru

Journal:

Journal of the American Chemical Society

Year:

1999

Language:

english

File:

PDF, 158 KB

english, 1999

39

Atomic-Scale Mechanism of the GTP → GDP Hydrolysis Reaction by the Giα1 Protein

Katagiri, Daisuke, Hata, Masayuki, Itoh, Takao, Neya, Sabro, Hoshino, Tyuji

Journal:

Journal of Physical Chemistry B

Year:

2003

Language:

english

File:

PDF, 538 KB

english, 2003

40

Synthesis, Structure, and Aromaticity of the Nickel(II) Complex of Pyricorrole, a Molecular Hybrid of Porphyrin and Corrole

Neya, Saburo, Suzuki, Masaaki, Matsugae, Takashi, Hoshino, Tyuji

Journal:

Inorganic Chemistry

Year:

2012

Language:

english

File:

PDF, 878 KB

english, 2012

41

Catalytic Mechanism of Class A β-Lactamase: Role of Lysine 73 and C3-Carboxyl Group of the Substrate Pen G in the Deacylation Step

Fujii, Yasuyuki, Hata, Masayuki, Hoshino, Tyuji, Tsuda, Minoru

Journal:

Journal of Physical Chemistry B

Year:

2002

Language:

english

File:

PDF, 247 KB

english, 2002

42

Computational Analysis of Stability of the β-Sheet Structure

Katagiri, Daisuke, Tsuchiya, Takahiro, Tsuda, Minoru, Hata, Masayuki, Hoshino, Tyuji

Journal:

Journal of Physical Chemistry B

Year:

2002

Language:

english

File:

PDF, 689 KB

english, 2002

43

Functional Evaluation of Iron Oxypyriporphyrin in Protein Heme Pocket

Neya, Saburo, Suzuki, Masaaki, Ode, Hirotaka, Hoshino, Tyuji, Furutani, Yuji, Kandori, Hideki, Hori, Hiroshi, Imai, Kiyohiro, Komatsu, Teruyuki

Journal:

Inorganic Chemistry

Year:

2008

Language:

english

File:

PDF, 457 KB

english, 2008

44

Computational Simulations of HIV-1 ProteasesMulti-drug Resistance Due to Nonactive Site Mutation L90M

Ode, Hirotaka, Neya, Saburo, Hata, Masayuki, Sugiura, Wataru, Hoshino, Tyuji

Journal:

Journal of the American Chemical Society

Year:

2006

Language:

english

File:

PDF, 603 KB

english, 2006

45

Computational Analysis of the Proton Translocation from Asp96 to Schiff Base in Bacteriorhodopsin

Sato, Yoshiharu, Hata, Masayuki, Neya, Saburo, Hoshino, Tyuji

Journal:

Journal of Physical Chemistry B

Year:

2006

Language:

english

File:

PDF, 672 KB

english, 2006

46

Resistant Mechanism against Nelfinavir of Human Immunodeficiency Virus Type 1 Proteases

Ode, Hirotaka, Ota, Masami, Neya, Saburo, Hata, Masayuki, Sugiura, Wataru, Hoshino, Tyuji

Journal:

Journal of Physical Chemistry B

Year:

2005

Language:

english

File:

PDF, 1.01 MB

english, 2005

47

Reduced Catalytic Activity of P450 2A6 Mutants with Coumarin: A Computational Investigation

Li, Weihua, Ode, Hirotaka, Hoshino, Tyuji, Liu, Hong, Tang, Yun, Jiang, Hualiang

Journal:

Journal of Chemical Theory and Computation

Year:

2009

Language:

english

File:

PDF, 3.38 MB

english, 2009

48

Structural and Energetic Analysis on the Complexes of Clinically Isolated Subtype C HIV-1 Proteases and Approved Inhibitors by Molecular Dynamics Simulation

Matsuyama, Shou, Aydan, Ay, Ode, Hirotaka, Hata, Masayuki, Sugiura, Wataru, Hoshino, Tyuji

Journal:

Journal of Physical Chemistry B

Year:

2010

Language:

english

File:

PDF, 4.35 MB

english, 2010

49

Analysis of the Unfolding Process of Green Fluorescent Protein by Molecular Dynamics Simulation

Hisatomi, Yoshihiro, Katagiri, Daisuke, Neya, Saburo, Hara, Masahiko, Hoshino, Tyuji

Journal:

Journal of Physical Chemistry B

Year:

2008

Language:

english

File:

PDF, 1.69 MB

english, 2008

50

Significance of the Molecular Shape of Iron Corrphycene in a Protein Pocket

Neya, Saburo, Imai, Kiyohiro, Hiramatsu, Yoshitsugu, Kitagawa, Teizo, Hoshino, Tyuji, Hata, Masayuki, Funasaki, Noriaki

Journal:

Inorganic Chemistry

Year:

2006

Language:

english

File:

PDF, 84 KB

english, 2006