Senior Scientist Suyong RE


2001 Ph.D. (Science) Rikkyo University, Japan.
1997 M.A. (Chemistry) Rikkyo University, Japan.
1994 B.S. (Chemistry) Korea University, Japan.
* 1998 Visiting student at Emory University, USA. (-1999)
* 1997 Visiting student at The University of Georgia, USA. (-1998)


2018-present Senior Scientist, RIKEN Center for Biosystems Dynamics Research
2016-2018 Senior Scientist, RIKEN Qiantitative Biology Center
2013-2016 Research Scientist, RIKEN
2011-2013 ASI Research Scientist, RIKEN Advanced Science Institute
2008-2011 Contract Researcher, RIKEN Advanced Science Institute
2007-2008 CNRS postdoctoral fellow (Ecole Normale Superieure, France)
2005-2007 JSPS postdoctoral fellowship for research abroad (Ecole Normale Superieure, France)
2003-2005 Postdoctoral fellow (Institute for Molecular Science, Japan)
2001-2003 JSPS postdoctoral fellowship (Institute for Molecular Science, Japan)


2013-2014 Lecturer (part-time), Kobe University, Japan.
2008-2015 Lecturer (part-time), Rikkyo University, Japan.


Chemical Society of Japan, The Biophysical Society of Japan, Japanese Society of Carbohydrate Research, Japan Society for Molecular Science, Theoretical Chemistry Society, BioSuperComputing Research Community


Bio-molecular science, computational chemistry

  1. Molecular modeling of protein phosphorylation using QM/MM method
  2. Glycan structure and function prediction using enhanced sampling method
  3. Hydration dynamics of bio-molecular systems


(Google Scholar profile)

Peer-reviewed journal articles

  1. Structural mechanisms underlying activity changes in an AMPA-type glutamate receptor induced by substitutions in its ligand-binding domain.
    Masayoshi Sakakura, Yumi Ohkubo, Hiraku Oshima, Suyong Re, Masahiro Ito, Yuji Sugita, and Hideo Takahashi.
    Structure, 27, 1698–1709 (2019)
  2. Replica-exchange umbrella sampling combined with Gaussian accelerated molecular dynamics for free-energy calculation of biomolecules.
    Hiraku Oshima, Suyong Re, Yuji Sugita.
    J. Chem. Theory Comput., 15, 5199-5208 (2019)
  3. Encounter complexes and hidden poses of kinase-inhibitor binding on the free-energy landscape.
    Suyong Re, Hiraku Oshima, Kento Kasahara, Motoshi Kamiya, and Yuji Sugita
    Proc. Natl. Acad. Sci. USA, 116, 18404-18409 (2019)
  4. De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations.
    Ai Niitsu, Suyong Re, Hiraku Oshima, Motoshi Kamiya, Yuji Sugita
    J. Chem. Inf. Model., 59, 3879-3888 (2019)
  5. Population Shift Mechanism for Partial Agonism of AMPA Receptor.
    Hiraku Oshima, Suyong Re, Masayoshi Sakakura, Hideo Takahashi, Yuji Sugita
    Biophys. J., 116, 57-68 (2019).
  6. Characterization of Conformational Ensembles of Protonated N-glycans in the Gas-Phase.
    Suyong Re, Shigehisa Watabe, Wataru Nishima, Eiro Muneyuki, Yoshiki Yamaguchi, Alexander D. MacKerell Jr. and Yuji Sugita
    Sci. Rep., 8, 1644 (2018).
  7. Enhanced Conformational Sampling of N-Glycans in Solution with Replica State Exchange Metadynamics.
    Raimondas Galvelis, Suyong Re, and Yuji Sugita.
    J. Chem. Theory Comput., 13, 1934–1942 (2017).
  8. Water Orientation at Ceramide/Water Interfaces Studied by Heterodyne-Detected Vibrational Sum Frequency Generation Spectroscopy and Molecular Dynamics Simulation.
    Aniruddha Adhikari, Suyong Re, Wataru Nishima, Mohammed Ahmed, Satoshi Nihonyanagi, Jeffery B. Klauda, Yuji Sugita, and Tahei Tahara.
    J. Phys. Chem. C, 120, 23692-23697 (2016).
  9. Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability.
    Dhilon S. Patel, Suyong Re, Emilia L. Wu, Yifei Qi, Phillip E. Klebba, Göran Widmalm, Min Sun Yeom, Yuji Sugita and Wonpil Im.
    Biophys. J., 110, 930-938 (2016).
  10. REIN: Replica-exchange INterface for simulating protein dynamics and function.
    Naoyuki Miyashita, Suyong Re, and Yuji Sugita.
    Int. J. Quantum Chem., 115, 325–332 (2015).
  11. Mosaic of Water Orientation Structures at a Neutral Zwitterion Lipid/Water Interface Revealed by Molecular Dynamics Simulations.
    Suyong Re, Wataru Nishima, Tahei Tahara and Yuji Sugita.
    J. Phys. Chem. Lett., 5, 4343-4348 (2014).
  12. CHARMM Force-Fields with Modified Polyphosphate Parameters Allow Stable Simulation of the ATP-Bound Structure of Ca2+-ATPase.
    Yasuaki Komuro, Suyong Re, Chigusa Kobayashi, Eiro Muneyuki, and Yuji Sugita.
    J. Chem. Theory Comput., 10, 4133−4142 (2014).
  13. Solvent Electronic Polarization Effects on Na+-Na+ and Cl--Cl- Pair Associations in Aqueous Solution.
    Cheol Ho Choi, Suyong Re, Mohammad H. O. Rashid, Hui Li, Michael Feig, and Yuji Sugita.
    J. Phys. Chem. B, 117, 9273-9279 (2013).
  14. Improved constrained optimization method for reaction-path determination in the generalized hybrid orbital quantum mechanical/molecular mechanical calculations.
    Jaewoon Jung, Suyong Re, Yuji Sugita, and Seiichiro Ten-no.
    J. Chem. Phys., 138, 044106 (2013).
  15. Interionic Hydration Structures of NaCl in Aqueous Solution: A Combined Study of Quantum Mechanical Cluster Calculations and QM/EFP-MD Simulations.
    Manik Ghosh, Suyong Re, Michael Feig, Yuji Sugita, Cheol Ho Choi.
    J. Phys. Chem. B, 117, 289-295 (2013).
  16. Confident identification of isomeric N-glycan structures by combined ion mobility mass spectrometry and hydrophilic interaction liquid chromatography.
    Yoshiki Yamaguchi, Wataru Nishima, Suyong Re, Yuji Sugita.
    Rapid Commun. Mass Spectrom., 26, 2877-84 (2012).
  17. 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.
    Chem. Phys. Lett., 539-540, 218-221 (2012).
  18. Effect of Bisecting GlcNAc and Core Fucosylation on Conformational Properties of Biantennary Complex-Type N-Glycans in Solution.
    Wataru Nishima, Naoyuki Miyashita, Yoshiki Yamaguchi, Yuji Sugita, and Suyong Re.
    J. Phys. Chem. B, 116, 8504-8512 (2012).
  19. Crystal structure of α5β1 integrin ectodomain: Atomic details of the fibronectin receptor.
    Masamichi Nagae, Suyong Re, Emiko Mihara, Terukazu Nogi, Yuji Sugita, and Junichi Takagi.
    J. Cell. Biol., 197, 131-140 (2012).
  20. Structural Diversity and Changes in Conformational Equilibria of Biantennary Complex-Type N-Glycans in Water Revealed by Replica-Exchange Molecular Dynamics Simulation.
    Suyong Re, Naoyuki Miyashita, Yoshiki Yamaguchi and Yuji Sugita.
    Biophys. J. (Letter), 101, L44-L46 (2011).
  21. Geometrically Associative Yet Electronically Dissociative Character in the Transition State of Enzymatic Reversible Phosphorylation.
    Suyong Re, Takashi Imai, Jaewoon Jung, Seiichiro Ten-no, and Yuji Sugita.
    J. Comput. Chem., 32, 260-270 (2011).
  22. Vibrational Symmetry Breaking of NO3- in Aqueous Solution: NO Asymmetric Stretch Frequency Distribution and Mean Splitting.
    Sai G. Ramesh, Suyong Re, Jean Boisson and James T. Hynes.
    J. Phys. Chem. A, 114, 1255-1269 (2010).
  23. A Two-dimensional energy surface of the phosphoryl transfer reaction catalyzed by phosphoserine phosphatase.
    Suyong Re, Jaewoon Jung, Seiichiro Ten-no, Yuji Sugita.
    Chem. Phys. Lett., 480, 284-288 (2009).
  24. Charge Transfer and OH Vibrational Frequency Red-Shifts in Nitrate-Water Clusters.
    Sai G. Ramesh, Suyong Re and James T. Hynes.
    J. Phys. Chem. A, 112, 3391-3398 (2008).
  25. On the Ultrafast Infrared Spectroscopy of Anion Hydration Shell Hydrogen Bond Dynamics.
    Bruno Nigro, Suyong Re, Damien Laage, Rossend Rey and James T. Hynes.
    J. Phys. Chem. A, 110, 11237-11243 (2006).
  26. Experimental Determination of the nN->σ*P-O Interaction Energy of O-Equatorial C-Apical Phosphoranes Bearing a Primary Amino Group.
    Takahiro Adachi, Shiro Matsukawa, Masaaki Nakamoto, Kazumasa Kajiyama, Satoshi Kojima, Yohsuke Yamamoto, Kin-ya Akiba, Suyong Re and Shigeru Nagase.
    Inorg. Chem., 45, 7269-7277 (2006).
  27. Interplay of single-wall carbon nanotubes and encapsulated La@C82, La2@C80, and Sc3N@C80,.
    Jing Lu, Shigeru Nagase, Suyong Re, Xinwei Zhang, Dapeng Yu, Jin Zhang, Rushan Han, Zhengxiang Gao, Hengqiang Ye, Shuang Zhang and Lianmao Peng.
    Phys. Rev. B, 71, 235417-235422 (2005).
  28. Ab Initio Molecular Orbital Investigation of a Precursor in Ethylene Biosynthesis: Proton Transfer in a Cluster of 1-Aminocyclopropane-1-carboxylic Acid and Water.
    Mika Ito, Suyong Re and Hiroaki Tokiwa.
    J. Phys. Chem. A, 108, 5417-5423 (2004).
  29. A Bowl-Shaped Fullerene Encapsulates a Water into the Cage.
    Sho-ichi Iwamatsu, Takashi Uozaki, Kaoru Kobayashi, Suyong Re, Shigeru Nagase and Shizuaki Murata.
    J. Am. Chem. Soc., 126, 2668-2669 (2004).
  30. How Is the CH/π Interaction Important for Molecular Recognition?
    Suyong Re and Shigeru Nagase.
    Chem. Commun., 6, 658-659 (2004).
  31. 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 and Keiji Morokuma.
    Theor. Chem. Acc., 112, 59-67 (2004).
  32. Theoretical Identification of C20 Carbon Clusters: Prevalence of the Monocyclic Isomer and Existence of the Smallest Fullerene and Bowl Isomer.
    Jing Lu, Suyong Re, Yoong-kee Choe, Shigeru Nagase, Yunsong Zhou, Rushan Han, Lianmao Peng, Xinwei Zhang and Xiangeng Zhao.
    Phys. Rev. B, 67, 125415 (2003).
  33. 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 and Shigeru Nagase.
    Chem. Phys. Lett., 369, 597-604 (2003).
  34. 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 and Hiroaki Tokiwa.
    Inorg. Chim. Acta, 340, 119-126 (2002).
  35. Characteristic Reactions and Properties of C-Apical O-Equatorial(O-cis) Spirophosphoranes: Effect of the σp-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.
    Shiro Matsukawa, Satoshi Kojima, Kazumasa Kajiyama, Yohsuke Yamamoto, Kin-ya Akiba, Suyong Re and Shigeru Nagase.
    J. Am. Chem. Soc., 124, 13154-13170 (2002).
  36. Effect of σP--O Orbital on Structure, Stereomutation, and Reactivity of C-Apical O-Equatorial Spirophosphoranes.
    Kin-ya Akiba, Shiro Matsukawa, Takahiro Adachi, Yohsuke Yamamoto, Suyong Re and Shigeru Nagase.
    Phosphorus,Sulfur, and Silicon and the Related Elements, 177, 1671-1675 (2002).
  37. Enhanced Stability of Non-Proton-Transferred Clusters of Hydrated Hydrogen Fluoride HF(H2O)n(n=1-7): A Molecular Orbital Study.
    Suyong Re.
    J. Phys. Chem. A, 105, 9725-9735 (2001).
  38. ONIOM Study of Chemical Reactions in Microsolvation Clusters:(H2O)nCH3Cl + OH¯(H2O)m (n+m=1 and 2).
    Suyong Re and Keiji Morokuma.
    J. Phys. Chem. A, 105, 7185-7197 (2001).
  39. Coexistence of Neutral and Ion-pair Clusters of Hydrated Sulfuric Acid H2SO4(H2O)n (n=1-5) -A Molecular Orbital Study.
    Suyong Re, Yoshihiro Osamura and Keiji Morokuma.
    J. Phys. Chem. A, 103, 3535-3547 (1999).
  40. Structures and Stability of Hydrated Clusters of Hydrogen Chloride, HCl(H2O)n , n=1-5.
    Suyong Re, Yoshihiro Osamura, Youhei Suzuki and Henry F. Schaefer.
    J. Chem. Phys., 109, 973-977 (1998).
  41. Size-Dependent Hydrogen-Bonds of Cluster Ions between Phenol Cation Radical and Water Molecules : A Molecular Orbital Study.
    Suyong Re and Yoshihiro Osamura.
    J. Phys. Chem. A, 102, 3798-3812 (1998).

Review articles

  1. Molecular Dynamics Simulation of Glycans.
    Suyong Re, Yoshiki Yamaguchi, Yuji Sugita.
    Trends Glycosci. Glycotechnol., (2019) DOI:DOI:10.4052/tigg.1616.1
  2. Conformational flexibility of N-glycans in solution studied by REMD simulations.
    Suyong Re, Wataru Nishima, Naoyuki Miyashita and Yuji Sugita.
    Biophys. Rev, 4, 179-187 (2012).
  3. Modeling the Transition State of Enzyme-Catalyzed Phosphoryl Transfer Reaction using QM/MM Method.
    Suyong Re and Yuji Sugita.
    YAKUGAKU ZASSHI, 131, 1171-1182 (2011).


  1. Replica-Exchange Methods for Biomolecular Simulations.
    Yuji Sugita, Motoshi Kamiya, Hiraku Oshima, Suyong Re.
    In: Bonomi M., Camilloni C. (eds) Biomolecular Simulations. Methods in Molecular Biology,, vol 2022, Humana, New York, NY (2019).

Conference proceedings / abstracts

  1. Simulations of biomolecules in cellular crowded environments.
    Yuji Sugita, Kento Kasahara, Hiraku Oshima, Isseki Yu, Grzegorz Nawrocki, Suyong Re, Michael Feig.
    J. Biomol. Struct. Dyn., 37, 51-52 (2019).
  2. Effects of T686A Mutation on the Structural Stability of the AMPA Receptor Ligand-Binding Domain.
    Hiraku Oshima, Suyong Re, Masayoshi Sakakura, Hideo Takahashi, Yuji Sugita.
    Biophys. J, 114, 125a (2018).
  3. Multiple Conformers and their Spectroscopic Properties of N-Glycan Predicted using Replica-Exchange Simulations.
    Wataru Nishima, Yoshiki Yamaguchi, Yuji Sugita and Suyong Re.
    Biophys. J, 102, 665a (2013).
  4. Improved Constrained Optimization Method for Reaction-Path Determination in Quantum Mechanical/Molecular Mechanical Calculations.
    Jaewoon Jung, Suyong Re, Yuji Sugita and Seiichiro Ten-no.
    Biophys. J, 104, 511a (2013).
  5. Conformational Diversity of N-Glycans in SolutionStudied by REMD Simulations.
    Yuji Sugita, Wataru Nishima, Yoshiki Yamaguchi and Suyong Re.
    Biophys. J, 104, 170a (2013).
  6. Modulation Mechanism on the Conforma-tional Diversities of Biantennary Complex-Type N-Glycans in Water.
    Wataru Nishima, Naoyuki Miyashita, Yoshiki Yamaguchi, Yuji Sugita and Suyong Re.
    Biophys. J, 102, 736a-737a (2012).
  7. Dynamical conformation of biantennary complex-type N-glycan in water revealed by using replica-exchange molecular dynamics simulations.
    Suyong Re, Naoyuki Miyashita, Yoshiki Yamaguchi and Yuji Sugita.
    Proceedings of From Computational Biophysics to Systems Biology (CBSB11), IAS Series, Vol. 8, 163-166 ISBN 978-3-89336-748-1 (2011).
  8. Hydration effects on water reorientation and ionic charge transfer.
    James T. Hynes, Damien Laage, Suyong Re and Sai. G. Ramesh.
    Abstracts of Papers of the American Chemical Society, 234, : Aug 19 (2007).

Press release etc.

  1. Faster modeling of interactions between ligands and proteins
    Research Highlight (Nov. 29, 2019).
  2. 酵素-阻害剤結合の初期会合体を予測 -初期結合過程を標的とした新たな創薬分子設計の可能性を拓く-
    理化学研究所 プレスリリース (2019年9月6日).
  3. 糖鎖構造から衝突断面積を予測-精密な糖鎖構造決定への新たな一歩-
    理化学研究所 プレスリリース (2018年2月5日).


  1. 理化学研究所杉田理論分子科学研究室
    アンサンブル, 16, 65-68 (2014).
  2. Meeting Report: Joint Seminar between RIKEN and Glycoinformatics Young Scientist Community.
    Suyong Re.
    Trends Glycosci. Glycotechnol., 26, 71-72 (2014).