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1

Modeling the Transition State of Enzyme-catalyzed Phosphoryl Transfer Reaction Using QM/MM Method

RE, Suyong, SUGITA, Yuji

Journal:

YAKUGAKU ZASSHI

Year:

2011

Language:

english

File:

PDF, 1.90 MB

english, 2011

2

carbon clusters: Prevalence of the monocyclic isomer and existence of the smallest fullerene and bowl isomer

Lu, Jing, Re, Suyong, Choe, Yoong-kee, Nagase, Shigeru, Zhou, Yunsong, Han, Rushan, Peng, Lianmao, Zhang, Xinwei, Zhao, Xiangeng

Journal:

Physical Review B

Year:

2003

Language:

english

File:

PDF, 363 KB

english, 2003

3

Structures and stability of hydrated clusters of hydrogen chloride, HCl(H[sub 2]O)[sub n], n=1–5

Re, Suyong, Osamura, Yoshihiro, Suzuki, Youhei, Schaefer, Henry F.

Journal:

The Journal of Chemical Physics

Year:

1998

Language:

english

File:

PDF, 382 KB

english, 1998

4

Calculation of packing structure of methanol solid using ab initio lattice energy at the MP2 level

Kanade Nagayoshi, Kazuo Kitaura, Shiro Koseki, Suyong Re, Kaoru Kobayashi, Yoong-Kee Choe, Shigeru Nagase

Journal:

Chemical Physics Letters

Year:

2003

Language:

english

File:

PDF, 315 KB

english, 2003

5

Experimental Determination of the n N → σ* P-O Interaction Energy of O-Equatorial C-Apical Phosphoranes Bearing a Primary Amino Group

Adachi, Takahiro, Matsukawa, Shiro, Nakamoto, Masaaki, Kajiyama, Kazumasa, Kojima, Satoshi, Yamamoto, Yohsuke, Akiba, Kin-ya, Re, Suyong, Nagase, Shigeru

Journal:

Inorganic Chemistry

Year:

2006

Language:

english

File:

PDF, 317 KB

english, 2006

6

3E1110 Replica-exchange interface program (REIN)(Proteins:Structure,Oral Presentation)

Miyashita, Naoyuki, Re, Suyong, Sugita, Yuji

Journal:

Seibutsu Butsuri

Year:

2012

Language:

english

File:

PDF, 210 KB

english, 2012

7

Charge Transfer and OH Vibrational Frequency Red Shifts in Nitrate−Water Clusters

Ramesh, Sai G., Re, Suyong, Hynes, James T.

Journal:

Journal of Physical Chemistry A

Year:

2008

Language:

english

File:

PDF, 161 KB

english, 2008

8

Replica-exchange umbrella sampling combined with Gaussian accelerated molecular dynamics for free-energy calculation of biomolecules

Oshima, Hiraku, Re, Suyong, Sugita, Yuji

Journal:

Journal of Chemical Theory and Computation

Year:

2019

Language:

english

File:

PDF, 942 KB

english, 2019

9

Conformational flexibility of N-glycans in solution studied by REMD simulations

Suyong Re, Wataru Nishima, Naoyuki Miyashita, Yuji Sugita

Journal:

Biophysical Reviews

Year:

2012

Language:

english

File:

PDF, 659 KB

english, 2012

10

Coexistence of Neutral and Ion-Pair Clusters of Hydrated Sulfuric Acid H 2 SO 4 (H 2 O) n ( n = 1−5)A Molecular Orbital Study

Re, Suyong, Osamura, Yoshihiro, Morokuma, Keiji

Journal:

Journal of Physical Chemistry A

Year:

1999

Language:

english

File:

PDF, 340 KB

english, 1999

11

Size-Dependent Hydrogen Bonds of Cluster Ions between Phenol Cation Radicals and Water Molecules: A Molecular Orbital Study

Re, Suyong, Osamura, Yoshihiro

Journal:

Journal of Physical Chemistry A

Year:

1998

Language:

english

File:

PDF, 343 KB

english, 1998

12

Multiple Conformers and their Spectroscopic Properties of N-Glycan Predicted using Replica-Exchange Simulations

Nishima, Wataru, Yamaguchi, Yoshiki, Sugita, Yuji, Re, Suyong

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 57 KB

english, 2013

13

CHARMM Force-Fields with Modified Polyphosphate Parameters Allow Stable Simulation of the ATP-Bound Structure of Ca 2+ -ATPase

Komuro, Yasuaki, Re, Suyong, Kobayashi, Chigusa, Muneyuki, Eiro, Sugita, Yuji

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 4.97 MB

english, 2014

14

How is the CH/? interaction important for molecular recognition?Electronic supplementary information (ESI) available: optimized cartesian coordinates. See http://www.rsc.org/suppdata/cc/b3/b316280j/

Re, Suyong, Nagase, Shigeru

Journal:

Chemical Communications

Year:

2004

Language:

english

File:

PDF, 304 KB

english, 2004

15

3D0936 Prediction of dynamical conformation of biantennary complex-type N-glycan in water by replica-exchange molecular dynamics simulations(3D Protein: Structure & Function 2,The 49th Annual Meeting of the Biophysical Society of Japan)

Re, Suyong, Miyashita, Naoyuki, Yamaguchi, Yoshiki, Sugita, Yuji

Journal:

Seibutsu Butsuri

Year:

2011

Language:

english

File:

PDF, 242 KB

english, 2011

16

Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability

Patel, Dhilon S., Re, Suyong, Wu, Emilia L., Qi, Yifei, Klebba, Phillip E., Widmalm, Göran, Yeom, Min Sun, Sugita, Yuji, Im, Wonpil

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 2.30 MB

english, 2016

17

3P111 Molecular dynamics simulations of SR Ca^-ATPase using improved ATP force field(03. Membrane proteins,Poster)

Komuro, Yasuaki, Kobayashi, Chigusa, Re, Suyong, Muneyuki, Eiro, Sugita, Yuji

Journal:

Seibutsu Butsuri

Year:

2013

Language:

english

File:

PDF, 695 KB

english, 2013

18

Enhanced Stability of Non-Proton-Transferred Clusters of Hydrated Hydrogen Fluoride HF(H 2 O) n ( n = 1−7): A Molecular Orbital Study

Journal:

Journal of Physical Chemistry A

Year:

2001

Language:

english

File:

PDF, 265 KB

english, 2001

19

Conformational Diversity of N-Glycans in Solution Studied by REMD Simulations

Sugita, Yuji, Nishima, Wataru, Yamaguchi, Yoshiki, Re, Suyong

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 35 KB

english, 2013

20

On the Ultrafast Infrared Spectroscopy of Anion Hydration Shell Hydrogen Bond Dynamics

Nigro, Bruno, Re, Suyong, Laage, Damien, Rey, Rossend, Hynes, James T.

Journal:

Journal of Physical Chemistry A

Year:

2006

Language:

english

File:

PDF, 126 KB

english, 2006

21

1P204 Structure and orientation of hydrating water molecules at phospholipid/water interface revealed by molecular dynamics simulation(13A. Biological & Artificial membrane: Structure & Property,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Re, Suyong, Nishima, Wataru, Tahara, Tahei, Sugita, Yuji

Journal:

Seibutsu Butsuri

Year:

2014

Language:

english

File:

PDF, 694 KB

english, 2014

22

Structural Mechanisms Underlying Activity Changes in an AMPA-type Glutamate Receptor Induced by Substitutions in Its Ligand-Binding Domain

Sakakura, Masayoshi, Ohkubo, Yumi, Oshima, Hiraku, Re, Suyong, Ito, Masahiro, Sugita, Yuji, Takahashi, Hideo

Journal:

Year:

2019

Language:

english

File:

PDF, 3.36 MB

english, 2019

23

1P105 Molecular dynamics simulations of ATP/ADP bound forms of SR Ca^-ATPase using CHARMM force field with modified polyphosphate parameters(03. Membrane proteins,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Komuro, Yasuaki, Re, Suyong, Kobayashi, Chigusa, Muneyuki, Eiro, Sugita, Yuji

Journal:

Seibutsu Butsuri

Year:

2014

Language:

english

File:

PDF, 696 KB

english, 2014

24

Mosaic of Water Orientation Structures at a Neutral Zwitterionic Lipid/Water Interface Revealed by Molecular Dynamics Simulations

Re, Suyong, Nishima, Wataru, Tahara, Tahei, Sugita, Yuji

Journal:

The Journal of Physical Chemistry Letters

Year:

2014

Language:

english

File:

PDF, 3.24 MB

english, 2014

25

Ab Initio Molecular Orbital Investigation of a Precursor in Ethylene Biosynthesis: Proton Transfer in a Cluster of 1-Aminocyclopropane-1-carboxylic Acid and Water

Ito, Mika, Re, Suyong, Tokiwa, Hiroaki

Journal:

Journal of Physical Chemistry A

Year:

2004

Language:

english

File:

PDF, 258 KB

english, 2004

26

Prediction of protein-ligand binding pose and affinity using gREST+FEP method

Oshima, Hiraku, Re, Suyong, Sugita, Yuji

Journal:

Journal of Chemical Information and Modeling

Year:

2020

File:

PDF, 2.05 MB

2020

27

Quantum mechanical/effective fragment potential molecular dynamics (QM/EFP-MD) study on intra-molecular proton transfer of glycine in water

Cheol Ho Choi, Suyong Re, Michael Feig, Yuji Sugita

Journal:

Chemical Physics Letters

Year:

2012

Language:

english

File:

PDF, 600 KB

english, 2012

28

A Bowl-Shaped Fullerene Encapsulates a Water into the Cage

Iwamatsu, Sho-ichi, Uozaki, Takashi, Kobayashi, Kaoru, Re, Suyong, Nagase, Shigeru, Murata, Shizuaki

Journal:

Journal of the American Chemical Society

Year:

2004

Language:

english

File:

PDF, 85 KB

english, 2004

29

Effect of σ* P--O Orbital on Structure, Stereomutation, and Reactivity of C -Apical O -Equatorial Spirophosphoranes

Akiba, Kin-ya, Matsukawa, Shiro, Adachi, Takahiro, Yamamoto, Yohsuke, Re, Suyong, Nagase, Shigeru

Journal:

Phosphorus Sulfur and Silicon and the Related Elements

Year:

2002

Language:

english

File:

PDF, 143 KB

english, 2002

30

Confident identification of isomeric N -glycan structures by combined ion mobility mass spectrometry and hydrophilic interaction liquid chromatography

Yamaguchi, Yoshiki, Nishima, Wataru, Re, Suyong, Sugita, Yuji

Journal:

Rapid Communications in Mass Spectrometry

Year:

2012

Language:

english

File:

PDF, 1.30 MB

english, 2012

31

Characteristic Reactions and Properties of C -Apical O -Equatorial ( O-cis ) Spirophosphoranes: Effect of the σ* P-O Orbital in the Equatorial Plane and Isolation of a Hexacoordinate Oxaphosphetane as an Intermediate of the Wittig Type Reaction of 10-P-5 Phosphoranes

Matsukawa, Shiro, Kojima, Satoshi, Kajiyama, Kazumasa, Yamamoto, Yohsuke, Akiba, Kin-ya, Re, Suyong, Nagase, Shigeru

Journal:

Journal of the American Chemical Society

Year:

2002

Language:

english

File:

PDF, 785 KB

english, 2002

32

1PT212 Effect of Bisecting GlcNAc and Core Fucosylation on Conformational Properties of Biantennary Complex-Type N-Glycans in Solution(The 50th Annual Meeting of the Biophysical Society of Japan)

Nishima, Wataru, Miyashita, Naoyuki, Yamaguchi, Yoshiki, Sugita, Yuji, Suyong, Re

Journal:

Seibutsu Butsuri

Year:

2012

Language:

english

File:

PDF, 213 KB

english, 2012

33

Molecular geometries, vibrational analysis, bonding and molecular orbitals of the three isomers of [RuCl(qn)2NO] (Hqn=2-methyl-8-quinolinol or 2-chloro-8-quinolinol): density functional theory studies

Hongfei Wang, Eiichi Miki, Suyong Re, Hiroaki Tokiwa

Journal:

Inorganica Chimica Acta

Year:

2002

Language:

english

File:

PDF, 200 KB

english, 2002

34

Structural Diversity and Changes in Conformational Equilibria of Biantennary Complex-Type N-Glycans in Water Revealed by Replica-Exchange Molecular Dynamics Simulation

Re, Suyong, Miyashita, Naoyuki, Yamaguchi, Yoshiki, Sugita, Yuji

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 381 KB

english, 2011

35

Exploring N-Glycan Conformers: Assessment of Enhanced Sampling Algorithms

Galvelis, Raimondas, Re, Suyong, Sugita, Yuji

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 40 KB

english, 2016

36

Population Shift Mechanism for Partial Agonism of AMPA Receptor

Oshima, Hiraku, Re, Suyong, Sakakura, Masayoshi, Takahashi, Hideo, Sugita, Yuji

Journal:

Biophysical Journal

Year:

2019

Language:

english

File:

PDF, 3.52 MB

english, 2019

37

ONIOM Study of Chemical Reactions in Microsolvation Clusters: (H 2 O) n CH 3 Cl + OH - (H 2 O) m ( n + m = 1 and 2)

Re, Suyong, Morokuma, Keiji

Journal:

Journal of Physical Chemistry A

Year:

2001

Language:

english

File:

PDF, 312 KB

english, 2001

38

Vibrational Symmetry Breaking of NO 3− in Aqueous Solution: NO Asymmetric Stretch Frequency Distribution and Mean Splitting †

Ramesh, Sai G., Re, Suyong, Boisson, Jean, Hynes, James T.

Journal:

Journal of Physical Chemistry A

Year:

2010

Language:

english

File:

PDF, 1.38 MB

english, 2010

39

Correction to “Mosaic of Water Orientation Structures at a Neutral Zwitterionic Lipid/Water Interface Revealed by Molecular Dynamics Simulations”

Re, Suyong, Nishima, Wataru, Tahara, Tahei, Sugita, Yuji

Journal:

The Journal of Physical Chemistry Letters

Year:

2015

File:

PDF, 121 KB

2015

40

3P314 Conformational analysis of PA-glycans by replica-exchange molecular dynamics simulations(30.Miscellaneous topics,Poster,The 51st Annual Meeting of the Biophysical Society of Japan)

Watanabe, Shigehisa, Re, Suyong, Muneyuki, Eiro, Sugita, Yuji

Journal:

Seibutsu Butsuri

Year:

2013

Language:

english

File:

PDF, 688 KB

english, 2013

41

A two-dimensional energy surface of the phosphoryl transfer reaction catalyzed by phosphoserine phosphatase

Suyong Re, Jaewoon Jung, Seiichiro Ten-no, Yuji Sugita

Journal:

Chemical Physics Letters

Year:

2009

Language:

english

File:

PDF, 798 KB

english, 2009

42

Own N-layered integrated molecular orbital and molecular mechanics study of the reaction of OH−with polychlorinated hydrocarbons CH(4−n)Cln(n=2–4)

Suyong Re, Keiji Morokuma

Journal:

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)

Year:

2004

Language:

english

File:

PDF, 525 KB

english, 2004

43

Modulation Mechanism on the Conformational Diversities of Biantennary Complex-Type N-Glycans in Water

Nishima, Wataru, Miyashita, Naoyuki, Yamaguchi, Yoshiyuki, Sugita, Yiji, Re, Suyong

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 61 KB

english, 2012

44

3C1148 New implementation of the reaction path determination in the QM/MM method(3C Protein: Funcrion 2,The 49th Annual Meeting of the Biophysical Society of Japan)

Jung, Jaewoon, Re, Suyong, Sugita, Yuji, Ten-no, Seiichiro

Journal:

Seibutsu Butsuri

Year:

2011

Language:

english

File:

PDF, 260 KB

english, 2011

45

Structural Mechanisms Underlying Activity Changes in an AMPA-type Glutamate Receptor Induced by Substitutions in Its Ligand-Binding Domain

Sakakura, Masayoshi, Ohkubo, Yumi, Oshima, Hiraku, Re, Suyong, Ito, Masahiro, Sugita, Yuji, Takahashi, Hideo

Journal:

Year:

2019

File:

PDF, 3.36 MB

2019

46

, and

Lu, Jing, Nagase, Shigeru, Re, Suyong, Zhang, Xinwei, Yu, Dapeng, Zhang, Jin, Han, Rushan, Gao, Zhengxiang, Ye, Hengqiang, Zhang, Shuang, Peng, Lianmao

Journal:

Physical Review B

Year:

2005

Language:

english

File:

PDF, 703 KB

english, 2005

47

Water Orientation at Ceramide/Water Interfaces Studied by Heterodyne-Detected Vibrational Sum Frequency Generation Spectroscopy and Molecular Dynamics Simulation

Adhikari, Aniruddha, Re, Suyong, Nishima, Wataru, Ahmed, Mohammed, Nihonyanagi, Satoshi, Klauda, Jeffery B., Sugita, Yuji, Tahara, Tahei

Journal:

The Journal of Physical Chemistry C

Year:

2016

Language:

english

File:

PDF, 1.67 MB

english, 2016

48

Characterization of Conformational Ensembles of Protonated N-glycans in the Gas-Phase

Re, Suyong, Watabe, Shigehisa, Nishima, Wataru, Muneyuki, Eiro, Yamaguchi, Yoshiki, MacKerell, Alexander D., Sugita, Yuji

Journal:

Scientific Reports

Year:

2018

Language:

english

File:

PDF, 3.86 MB

english, 2018

49

De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations

Niitsu, Ai, Re, Suyong, Oshima, Hiraku, Kamiya, Motoshi, Sugita, Yuji

Journal:

Journal of Chemical Information and Modeling

Year:

2019

File:

PDF, 1.30 MB

2019

50

Encounter complexes and hidden poses of kinase-inhibitor binding on the free-energy landscape

Re, Suyong, Oshima, Hiraku, Kasahara, Kento, Kamiya, Motoshi, Sugita, Yuji

Journal:

Proceedings of the National Academy of Sciences

Year:

2019

Language:

english

File:

PDF, 1.45 MB

english, 2019

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