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1

Fragment molecular orbital method: use of approximate electrostatic potential

Tatsuya Nakano, Tsuguchika Kaminuma, Toshiyuki Sato, Kaori Fukuzawa, Yutaka Akiyama, Masami Uebayasi, Kazuo Kitaura

Journal:

Chemical Physics Letters

Year:

2002

Language:

english

File:

PDF, 179 KB

english, 2002

2

Fragment molecular orbital method: an approximate computational method for large molecules

Kazuo Kitaura, Eiji Ikeo, Toshio Asada, Tatsuya Nakano, Masami Uebayasi

Journal:

Chemical Physics Letters

Year:

1999

Language:

english

File:

PDF, 197 KB

english, 1999

3

Fast and accurate molecular dynamics simulation of a protein using a special-purpose computer

Komeiji, Yuto, Uebayasi, Masami, Takata, Ryo, Shimizu, Akihiro, Itsukashi, Keiji, Taiji, Makoto

Journal:

Journal of Computational Chemistry

Year:

1997

Language:

english

File:

PDF, 428 KB

english, 1997

4

Computational design of a substrate specificity mutant of a protein

Honda, Nobuo, Komeiji, Yuto, Uebayasi, Masami, Yamato, Ichiro

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1996

Language:

english

File:

PDF, 548 KB

english, 1996

5

Ab initio quantum mechanical study of the binding energies of human estrogen receptor α with its ligands: An application of fragment molecular orbital method

Kaori Fukuzawa, Kazuo Kitaura, Masami Uebayasi, Kotoko Nakata, Tsuguchika Kaminuma, Tatsuya Nakano

Journal:

Journal of Computational Chemistry

Year:

2005

Language:

english

File:

PDF, 623 KB

english, 2005

6

Ab initio fragment molecular orbital (FMO) method applied to analysis of the ligand–protein interaction in a pheromone-binding protein

Tadashi Nemoto, Dmitri G. Fedorov, Masami Uebayasi, Kenji Kanazawa, Kazuo Kitaura, Yuto Komeiji

Journal:

Computational Biology and Chemistry

Year:

2005

Language:

english

File:

PDF, 343 KB

english, 2005

7

Fragment molecular orbital method: application to polypeptides

Tatsuya Nakano, Tsuguchika Kaminuma, Toshiyuki Sato, Yutaka Akiyama, Masami Uebayasi, Kazuo Kitaura

Journal:

Chemical Physics Letters

Year:

2000

Language:

english

File:

PDF, 113 KB

english, 2000

8

Fragment molecular orbital method: application to molecular dynamics simulation, ‘ab initio FMO-MD’

Yuto Komeiji, Tatsuya Nakano, Kaori Fukuzawa, Yutaka Ueno, Yuichi Inadomi, Tadashi Nemoto, Masami Uebayasi, Dmitri G. Fedorov, Kazuo Kitaura

Journal:

Chemical Physics Letters

Year:

2003

Language:

english

File:

PDF, 206 KB

english, 2003

9

Pair interaction molecular orbital method: an approximate computational method for molecular interactions

Kazuo Kitaura, Takuya Sawai, Toshio Asada, Tatsuya Nakano, Masami Uebayasi

Journal:

Chemical Physics Letters

Year:

1999

Language:

english

File:

PDF, 143 KB

english, 1999

10

A molecular dynamics study of solvent behavior around a protein

Yuto Komeiji, Masami Uebayasi, Jun-ichiro Someya, Ichiro Yamato

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1993

Language:

english

File:

PDF, 688 KB

english, 1993

11

Molecular dynamics simulations of trp apo-and holorepressors: Domain structure and ligand–protein interaction

Yuto Komeiji, Masami Uebayasi, Ichiro Yamato

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1994

Language:

english

File:

PDF, 874 KB

english, 1994

12

Fragment molecular orbital method: analytical energy gradients

Kazuo Kitaura, Sin-Ichirou Sugiki, Tatsuya Nakano, Yuto Komeiji, Masami Uebayasi

Journal:

Chemical Physics Letters

Year:

2001

Language:

english

File:

PDF, 122 KB

english, 2001

13

Computational Observation of an Ion Permeation Through a Channel Protein

Atushi Suenaga, Yuto Komeiji, Masami Uebayasi, Toshiyuki Meguro, Minoru Saito, Ichiro Yamato

Journal:

Bioscience Reports

Year:

1998

Language:

english

File:

PDF, 930 KB

english, 1998

14

Purification and properties of 4-hydroxycyclohexanecarboxylate dehydrogenase from Corynebacterium cyclohexanicum

Hitoshi OBATA, Masami UEBAYASI, Toshi KANEDA

Journal:

Year:

1988

Language:

english

File:

PDF, 824 KB

english, 1988

15

Enantiotopic differentiation in horse-liver alcohol-dehydrogenase-catalyzed oxidoreduction studied with novel substrates having organometallic moieties

Yoshimitsu YAMAZAKI, Masami UEBAYASI, Kuniaki HOSONO

Journal:

Year:

1989

Language:

english

File:

PDF, 448 KB

english, 1989

16

Enantiotopic differentiation in horse-liver alcohol-dehydrogenase-catalyzed oxidoreduction studied with novel substrates having organometallic moieties

Yoshimitsu YAMAZAKI, Masami UEBAYASI, Kuniaki HOSONO

Journal:

Year:

1989

Language:

english

File:

PDF, 993 KB

english, 1989

17

RNA hydrolysis via an oxyphosphorane intermediate

Tadafumi Uchimaru, Joey W. Storer, Kazutoshi Tanabe, Masami Uebayasi, Satoshi Nishikawa, Kazunari Taira

Journal:

Biochemical and Biophysical Research Communications

Year:

1992

Language:

english

File:

PDF, 422 KB

english, 1992

18

Induction of adiponectin by natural and synthetic phenolamides in mouse and human preadipocytes and its enhancement by docosahexaenoic acid

Yoshimitsu Yamazaki, Yasuhiro Kawano, Masami Uebayasi

Journal:

Year:

2008

Language:

english

File:

PDF, 1.14 MB

english, 2008

19

Molecular dynamics simulations revealed Ca2+-dependent conformational change of Calmodulin

Yuto Komeiji, Yutaka Ueno, Masami Uebayasi

Journal:

Year:

2002

Language:

english

File:

PDF, 434 KB

english, 2002

20

Corrigendum to: Molecular dynamics simulations revealed Ca2+-dependent conformational change of Calmodulin (FEBS 26172): [FEBS Letters 521 (2002) 133–139]

Yuto Komeiji, Yutaka Ueno, Masami Uebayasi

Journal:

Year:

2002

Language:

english

File:

PDF, 43 KB

english, 2002

21

Change in Conformation by DNA-Peptide Association: Molecular Dynamics of the Hin-Recombinase–hixL Complex

Komeiji, Yuto, Uebayasi, Masami

Journal:

Biophysical Journal

Year:

1999

Language:

english

File:

PDF, 684 KB

english, 1999

22

Energetics of RNA cleavage: implications for the mechanism of action of ribozymes

Taira, Kazunari, Uebayasi, Masami, Maeda, Hidekatsu, Furukawa, Kensuke

Journal:

Protein Engineering Design and Selection

Year:

1990

Language:

english

File:

PDF, 4.76 MB

english, 1990

23

The Fragment Molecular Orbital Method for Geometry Optimizations of Polypeptides and Proteins

Fedorov, Dmitri G., Ishida, Toyokazu, Uebayasi, Masami, Kitaura, Kazuo

Journal:

Journal of Physical Chemistry A

Year:

2007

Language:

english

File:

PDF, 711 KB

english, 2007

24

Existence of a marginally stable intermediate during the base-catalyzed methanolysis of methylene phosphate and ab initio studies of the monohydration of the pentacoordinated oxyphosphorane intermediate

Storer, Joey W., Uchimaru, Tadafumi, Tanabe, Kazutoshi, Uebayasi, Masami, Nishikawa, Satoshi, Taira, Kazunari

Journal:

Journal of the American Chemical Society

Year:

1991

Language:

english

File:

PDF, 896 KB

english, 1991

25

Properties of dianionic oxyphosphorane intermediates: implication to the reaction profile for base-catalyzed RNA hydrolysis

Taira, Kazunari, Uchimaru, Tadafumi, Storer, Joey W., Yliniemela, Ari, Uebayasi, Masami, Tanabe, Kazutoshi

Journal:

Journal of Organic Chemistry

Year:

1993

Language:

english

File:

PDF, 1.35 MB

english, 1993

26

Theoretical and Experimental Considerations on the Hammerhead Ribozyme Reactions: Divalent Magnesium Ion Mediated Cleavage of Phosphorus-Oxygen Bonds

Uebayasi, Masami, Uchimaru, Tadafumi, Sawata, Shinya, Shimayama, Takashi, Taira, Kazunari, Koguma, T.

Journal:

Journal of Organic Chemistry

Year:

1994

Language:

english

File:

PDF, 2.10 MB

english, 1994

27

Electrostatic Interactions That Determine the Rate of Pseudorotation Processes in Oxyphosphorane Intermediates: Implications with Respect to the Roles of Metal Ions in the Enzymatic Cleavage of RNA

Uchimaru, Tadafumi, Uebayasi, Masami, Hirose, Takuji, Tsuzuki, Seiji, Yliniemelä, Ari, Tanabe, Kazutoshi, Taira, Kazunari

Journal:

Journal of Organic Chemistry

Year:

1996

Language:

english

File:

PDF, 265 KB

english, 1996

28

Molecular Dynamics Simulation of the Hin-Recombinase—DNA Complex

Komeiji, Yuto, Uebayasi, Masami

Journal:

Molecular Simulation

Year:

1999

Language:

english

File:

PDF, 1.19 MB

english, 1999

29

Free energy perturbation study on a Trp-binding mutant (Ser 88 →Cys) of the trp -repressor

Komeiji, Yuto, Uebayasi, Masami, Someya, Jun-ichiro, Yamato, Ichiro

Journal:

Protein Engineering Design and Selection

Year:

1992

Language:

english

File:

PDF, 685 KB

english, 1992

30

Cyclic oxyphosphoranes as model intermediates during splicing and cleavage or RNA: Ab initio molecular orbital calculations on the conformational analysis

Taira, Kazunari, Uebayasi, Masami, Furukawa, Kensuke

Journal:

Nucleic Acids Research

Year:

1989

Language:

english

File:

PDF, 1.44 MB

english, 1989

31

Molecular dynamics simulation of trp -aporepressor in a solvent

Komeiji, Yuto, Uebayasi, Masami, Someya, Jun-ichiro, Yamato, Ichiro

Journal:

Protein Engineering Design and Selection

Year:

1991

Language:

english

File:

PDF, 461 KB

english, 1991

32

Incorporation of [ 14 C]Methanol and [ 14 C]Bicarbonate by Hyphomicrobium sp. 53-49 under Various Growth Conditions: Aerobic, Denitrifying and Autotrophic

Uebayasi, Masami, Kawamura, Sugio, Tomizuka, Noboru, Kamibayashi, Akira, Tonomura, Kenzo

Journal:

Agricultural and Biological Chemistry

Year:

1984

Language:

english

File:

PDF, 2.13 MB

english, 1984

33

Determination of the Absolute Configuration of (−)-2,2,2-(Trifluoro-1-hydroxyethyl)ferrocene

Goto, Midori, Yamazaki, Yoshimitsu, Uebayasi, Masami

Journal:

Bulletin of the Chemical Society of Japan

Year:

1993

File:

PDF, 508 KB

1993

34

Prediction of Endocrine Disruptors Based on a New Structure-Activity Relationship for Sex and Environmental Hormones Using Chemical Hardness Concept.

KOBAYASHI, Shigeki, SUGAYA, Toshiya, SAKATA, Nobuo, UEBAYASI, Masami, SAMESHIMA, Keiichiro, TANAKA, Akira

Journal:

CHEMICAL & PHARMACEUTICAL BULLETIN

Year:

2001

Language:

english

File:

PDF, 119 KB

english, 2001

35

Autotrophic growth of a Hyphomicrobium sp. and its hydrogenase activity.

UEBAYASI, Masami, TOMIZUKA, Noboru, KAMIBAYASHI, Akira, TONOMURA, Kenzo

Journal:

Agricultural and Biological Chemistry

Year:

1981

Language:

english

File:

PDF, 423 KB

english, 1981

36

Incorporation of (14C)methanol and (14C)bicarbonate by Hyphomicrobium sp. 53-49 under various growth conditions: Aerobic, denitrifying and autotrophic.

UEBAYASI, Masami, KAWAMURA, Sugio, TOMIZUKA, Noboru, KAMIBAYASHI, Akira, TONOMURA, Kenzo

Journal:

Agricultural and Biological Chemistry

Year:

1984

Language:

english

File:

PDF, 2.23 MB

english, 1984

37

Stereoselectivity of the enzymatic reduction of aldehydic and ketonic carbonyl groups in planar chiral organomanganese complexes.

YAMAZAKI, Yoshimitsu, UEBAYASI, Masami, SOMEYA, Jun-ichiro, HOSONO, Kuniaki

Journal:

Agricultural and Biological Chemistry

Year:

1990

Language:

english

File:

PDF, 960 KB

english, 1990

38

Comparison of the key enzymes of Hyphomicrobium sp. 53-49 under various growth conditions: Aerobic, denitrifying and autotrophic.

UEBAYASI, Masami, KAWAMURA, Sugio, TOMIZUKA, Noboru, KAMIBAYASHI, Akira

Journal:

Agricultural and Biological Chemistry

Year:

1985

Language:

english

File:

PDF, 1.33 MB

english, 1985

39

3D Structure Based Atomic Charge Calculation for Molecular Mechanics and Molecular Dynamics Simulations

Nakano, Tatsuya, Kaminuma, Tsuguchika, Uebayasi, Masami, Nakata, Yoshiro

Journal:

Chem-Bio Informatics Journal

Year:

2001

Language:

english

File:

PDF, 35 KB

english, 2001