Publications

Journal articles

2021

  1. D.Takaya, C.Watanabe, S.Nagase, K.Kamisaka, Y.Okiyama, H.Moriwaki, H.Yuki, T.Sato, N.Kurita, Y.Yagi, T.Takagi, N.Kawashita, K.Takaba, T.Ozawa, M.Takimoto-Kamimura, S.Tanaka, K.Fukuzawa, and T.Honma
    “FMODB: The World’s First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method” J. Chem. Inf. Model., 61, 777-794 (2021). https://doi.org/10.1021/acs.jcim.0c01062
  2. S.Nakamura, R.Saito, S.Yamamoto, I.Kobayashi, R.Takeda, R.Suzuki, K.Kawai, M.Takimoto-Kamimura, and N.Kurita “Proposal of novel potent inhibitors against androgen receptor based on ab initio molecular orbital calculations” J. Mol. Graph. Model. 105, 107873 (2021). https://doi: 10.1016/j.jmgm.2021.107873
  3. K. Watanabe, C. Watanabe,T. Honma, Y. Tian, Y. Kawashima, N. Kawashita, K. Fukuzawa, and T. Takagi “Computational ab initio interaction analyses between neutralizing antibody and SARS-CoV-2 variant spike proteins using the fragment molecular orbital method” Bull. Chem. Soc. Jpn. Advance publication (2021).
    https://doi.org/10.1246/bcsj.20210104
  4. T. Takei, J. Takayama, M. Xuan, M. Tomoda, H. Miyamae, and T. Sakamoto “A study of enantioselective syntheses by Sharpless asymmetric oxidation for aryl sulfoxides containing oxygen groups at the ortho position” J. Chem. Sci.,133, 28 (2021). https://doi.org/10.1007/s12039-021-01887-5
  5. Y. Okiyama, Y. Mochizuki, M. Yamanaka, and S. Tanaka ”Density-Matrix Based Scheme of Basis Selection for Linear Combination of Fragment Molecular Orbitals” J. Phys. Soc. Jpn., 90, 064301 (2021). https://doi.org/10.7566/JPSJ.90.064301
  6. S.Nakamura, R.Saito, S.Yamamoto, Y.Terauchi, A.Kittaka, M.Takimoto-Kamimura, and N.Kurita “Proposal of novel inhibitors against vitamin-D receptor: molecular docking, molecular mechanics and ab initio molecular orbital simulations” Biophys. Chem., 270, 106540 (2021). https://doi:10.1016/j.bpc.2020.106540
  7. D. Takaya, C. Watanabe, S. Nagase, K. Kamisaka, Y. Okiyama, H. Moriwaki, H. Yuki, T. Sato, N. Kurita, Y. Yagi, T. Takagi, N. Kawashita, K. Takaba, T. Ozawa, M. Takimoto-Kamimura, S. Tanaka, K. Fukuzawa, and T. Honma“ FMODB: The World’s First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method” J. Chem. Inf. Model., 61, 777-794(2021). https://doi.org/10.1021/acs.jcim.0c01062
  8. C. Watanabe, Y. Okiyama, S. Tanaka, K. Fukuzawa, and T. Honma“Molecular Recognition of SARS-CoV-2 Spike Glycoprotein: Quantum Chemical Hot Spot and Epitope Analyses” Chem. Sci., 12, 4722-4739 (2021). https://doi.org/ 10.1039/D0SC06528E
  9. K. Watanabe, C. Watanabe, T. Honma, Y. Tian, Y. Kawashima, N. Kawashita, T. Takagi, and K. Fukuzawa “Intermolecular Interaction Analyses on SARS-CoV-2 Receptor Binding Domain and Human Angiotensin-Converting Enzyme 2 Receptor-Blocking Antibody/peptide Using Fragment Molecular Orbital Calculation” J. Phys. Chem. Lett., 12, 4059-4066 (2021). https://doi.org/ 10.1021/acs.jpclett.1c00663

2020

  1. K. Kato, T. Masuda, C. Watanabe, N. Miyagawa, H.vMizouchi, S. Nagase, K. Kamisaka, K. Oshima, S. Ono, H. Ueda, A. Tokuhisa, R. Kanada, M. Ohta, M. Ikeguchi, Y. Okuno, K. Fukuzawa, and T. Honma “High-Precision Atomic Charge Prediction for Protein Systems Using Fragment Molecular Orbital Calculation and Machine Learning”  J. Chem. Inf. Model., 60, 7, 3361-3368 (2020). https://doi.org/10.1021/acs.jcim.0c00273
  2. S.Suzuki, T. Nakamura, R. Saito, Y.Terauchi, K. Kawai, M.Takimoto-Kamimura, and N.Kurita “Structural change of retinoic-acid receptor-related orphan receptor induced by binding of inverse-agonist: Molecular dynamics and ab initio molecular orbital simulations”  Comput. Struct .Biol J.,18, 1676-1685(2020).
    (https://doi.org/10.1016/j.csbj.2020.06.034)
  3. K.Kato, T.Honma, and K.Fukuzawa “Intermolecular interaction among Remdesivir, RNA and RNAdependent RNA polymerase of SARS-CoV-2 analyzed by fragment molecular orbital calculation”  J.Mol.Graph.Model., 100_107695 (2020). https://doi.org/10.1016/j.jmgm.2020.107695
  4. S. Tanaka, C. Watanabe, T. Honma, K. Fukuzawa, K. Ohishi, and T. Maruyama “Identification of Correlated Inter-Residue Interactions in Protein Complex Based on the Fragment Molecular Orbital Method”  J. Mol. Graph. Model., 100,107650 (2020). https://doi.org/10.1016/j.jmgm.2020.107650
  5. S. Tokutomi, K. Shimamura, K. Fukuzawa, and S. Tanaka “Machine Learning Prediction of Inter-Fragment Interaction Energies between Ligand and Amino-Acid Residues on the Fragment Molecular Orbital Calculations for Janus Kinase – Inhibitor Complex”  Chem. Phys. Lett., 757,137883 (2020). https://doi.org/10.1016/j.cplett.2020.137883
  6. S. Tanaka, C. Watanabe, T. Honma, K. Fukuzawa, K. Ohishi, and T. Maruyama “Identification of Correlated Inter-Residue Interactions in Protein Complex Based on the Fragment Molecular Orbital Method” J. Mol. Graph., Model. 100,107650 (2020). https://doi.org/10.1016/j.jmgm.2020.107650
  7. S. Tokutomi, K. Shimamura, K. Fukuzawa, and S. Tanaka”Machine Learning Prediction of Inter-Fragment Interaction Energies between Ligand and Amino-Acid Residues on the Fragment Molecular Orbital Calculations for Janus Kinase-Inhibitor Complex” Chem. Phys. Lett., 757, 137883(2020). https://doi.org/10.1016/j.cplett.2020.137883
  8. K. Kato, T. Masuda, C. Watanabe, N. Miyagawa, H. Mizouchi, S. Nagase, K. Kamisaka, K. Oshima, S. Ono, H Ueda, A. Tokuhisa, R. Kanada. M. Ohta, M. Ikeguchi, Y. Okuno, K. Fukuzawa, and T. Honma
    “High-Precision Atomic Charge Prediction for Protein Systems Using Fragment Molecular Orbital Calculation and Machine Learning” J. Chem. Inf. Model., 60, 3361-3368 (2020). https://pubs.acs.org/doi/10.1021/acs.jcim.0c00273
  9. K. Kato, T. Honma, and K. Fukuzawa “Intermolecular Interaction Among Remdesivir, RNA and RNA-Dependent RNA Polymerase of SARS-CoV-2 Analyzed by Fragment Molecular Orbital Calculation” J. Mol. Graph. Model., 100, 107695-107699 (2020). https://doi.org/10.1016/j.jmgm.2020.107695

2019

  1. Y. Terauchi, R. Suzuki, R.Takeda, I. Kobayashi, A. Kittaka, M. Takimoto-Kamimura and N. Kurita “Ligand chirality can affect histidine protonation of vitamin-D receptor: ab initio molecular orbital calculations in water” J. Steroid Biochem. Mol. Biol., 186, 89-95 (2019) . https://doi.org/10.1016/j.jsbmb.2018.09.020
  2. C. Watanabe, H. Watanabe, Y. Okiyama, D. Takaya, K. Fukuzawa, S. Tanaka and T. Honma “Development of an automated fragment molecular orbital (FMO) calculation protocol toward construction of quantum mechanical calculation database for large biomolecules” Chem-Bio Informatics J., 19, 5-18 (2019).  https://doi.org/10.1273/cbij.19.5
  3. F. Shirai, T. Tsumura, Y. Yashiroda, Y. Yuki , H. Niwa, S. Sato, T. Chikada, Y.Koda,  K.Washizuka,     N. Yoshimoto, M.  Shitara,  Y. Muramatsu, H. Yoshida, A. Mizutani, H. Seimiya, M. Yoshida  and H. Koyama “Discovery of Novel Spiroindoline Derivatives as Selective Tankyrase Inhibitors” J. Med. Chem., 62, 3407–3427 (2019). https://doi.org/10.1021/acs.jmedchem.8b01888

2018

  1. R. Takeda, R. Suzuki, I. Kobayashi, K. Kawai,  A. Kittaka,  M. Takimoto-Kamimura and N. Kurita “Specific interactions between vitamin D receptor and ligand depending on its chirality: ab initio fragment molecular orbital calculations” Chem-Bio Informatics J., 18, 32-43 (2018). https://doi.org/10.1273/cbij.18.32
  2. Y. Yagi, T. Kimura, M, Kamezawa, Y. Naoshima “Biomolecular Chemical Simulations toward Elucidation of  the Enantioselectivity and Reactivity of Lipases in Organic Synthesis” Chem-Bio Informatics Journal, 18, 21-31 (2018). https://doi.org/10.1273/cbij.18.21
  3. R. Takeda, I. Kobayashi, R. Suzuki, K. Kawai, A. Kittaka, M. Takimoto-Kamimura and N. Kurita “Proposal of potent inhibitors for vitamin-D receptor based on ab initio fragment molecular orbital calculations”  J. Mol. Graph. Model., 80, 320-326 (2018). https://doi.org/10.1016/j.jmgm.2018.01.014
  4. Y. Tsuchiya, Y. Namiuchi, H. Wako, and H. Tsurui  “A study of CDR3 loop dynamics reveals distinct mechanisms of peptide recognition by Tcell receptors exhibiting different levels of crossreactivity”  Immunology, 153, 466-478 (2018). https://doi.org/10.1111/imm.12849
  5. K. Maruyama, Y. Sheng, H. Watanabe, K. Fukuzawa, and S. Tanaka  “Application of Singular Value Decomposition to the Inter-Fragment Interaction Energy Analysis for Ligand Screening”  Comput. Theor. Chem., 1132, 23-34 (2018). https://doi.org/10.1016/j.comptc.2018.04.001
  6. Y. Komeiji, Y. Okiyama, Y. Mochizuki, and K. Fukuzawa “Interaction between a single-stranded DNA and a binding protein viewed by the fragment molecular orbital method” Bull. Chem. Soc. Jpn., 91, 1596-1605 (2018). https://doi.org/10.1246/bcsj.20180150
  7. Y. Sheng, H. Watanabe, K. Maruyama, C. Watanabe, Y. Okiyama, T. Honma, K.  Fukuzawa, and S. Tanaka “Towards good correlation between fragment molecular orbital interaction energies and experimental IC50 for ligand binding:A case study of p38 MAP kinase” Comput. Struct. Biotechnol. J., 16, 421-434 (2018).  https://doi.org/10.1016/j.csbj.2018.10.003
  8. H. Seki, T. Kato, T. Furuishi, K. Fukuzawa, and E. Yonemochi “Ligand binding specificity analysis of estrogen receptor by FMO method”  J. Comput. Chem. Jpn., 17, 160-162 (2018). https://doi.org/10.2477/jccj.2018-0028  In Japanese,  関 祐哉, 加藤 司, 古石 誉之, 福澤 薫, 米持 悦生「FMO法によるエストロゲン受容体のリガンド結合特異性解析」
  9.  F. Xu, S. Tanaka, H. Watanabe, Y. Shimane, M. Iwasawa, K. Ohishi, and T. Maruyama “Computational Analysis of the Interaction Energies between Amino Acid Residues of the Measles Virus Hemagglutinin and Its Receptors”  Viruses, 10, 236  (2018). https://doi.org/10.3390/v10050236
  10. D.Takaya, K.Inaka,  A .Omura, K .Takenuki, M .Kawanishi, Y .Yabuki, Y.Nakagawa, K. Tsuganezawa, N .Ogawa, C .Watanabe, T .Honma, K .Aritake, Y .Urade, M .Shirouzu, and  A.Tanaka. “Characterization of crystal water molecules in a high-affinity inhibitor and hematopoietic prostaglandin D synthase complex by interaction energy studies” Bioorg. Med. Chem., 26, 4726-4734 (2018). https://doi.org/10.1016/j.bmc.2018.08.014

2017

  1. K. Shimamura, H. Ishimura, I. Kobayashi, R. Kadoya, K. Kawai, M. Takimoto-Kamimura, and N. Kurita “Molecular dynamics and ab initio FMO calculations on the effect of water molecules on the interactions between androgen receptor and its ligand and cofactor” Proceedings of The 2016 International Conference On Advanced Informatics, 2016, Penang, Malaysia. https://doi.org/10.1109/ICAICTA.2016.7803095
  2.  I. Kobayashi, K. Shimamura, H. Ishimura, R. Kadoya, K. Kawai, M. Takimoto-Kamimura, and N. Kurita “Effect of cofactor-binding on the specific interactions between androgen receptor and its ligand: ab initio molecular simulations” Proceedings of The 2016 International Conference On Advanced Informatics, 2016, Penang, Malaysia. (https://doi.org/10.1109/ICAICTA.2016.7803088)
  3. R. Takeda, I. Kobayashi, K. Shimamura, H. Ishimura, R. Kadoya, K. Kawai, A. Kittaka, M. Takimoto-Kamimura and, N. Kurita “Specific interactions between vitamin-D receptor and its ligands: ab initio molecular orbital calculations in water” J. Steroid Biochem. Mol. Biol., 171, 75-79 (2017). https://doi.org/10.1016/j.jsbmb.2017.02.018
  4. K. Fukuzawa “Protein-ligand interaction analysis based on quantum theory – Efforts to implement FMO drug discovery” Folia Pharmacol. Jpn. 149, 240-246 (2017). https://doi.org/10.1254/fpj.149.240  In Japanese, 福澤薫「量子論に基づくタンパク質―化学物質相互作用解析~FMO創薬の実現に向けた取り組み」日本薬理学雑誌 
  5. S. Uehara, S. Tanaka “Cosolvent-Based Molecular Dynamics for Ensemble Docking: Practical Method for Generating Druggable Protein Conformations” J. Chem. Inf. Model., 57, 742-756  (2017). https://doi.org/10.1021/acs.jcim.6b00791
  6. M. Ozawa, T. Ozawa, and K. Ueda “Application of the fragment molecular orbital method analysis to fragment-based drug discovery of BET (bromodomain and extra-terminal proteins) inhibitors” J. Mol. Graph. Model., 74, 73-82 (2017). https://doi.org/10.1016/j.jmgm.2017.02.013
  7. M. Ozawa, T. Ozawa, M. Nishio, and K. Ueda “The role of CH/π interactions in the high affinity binding of streptavidin and biotin” J. Mol. Graph. Model., 75, 117-124 (2017). https://doi.org/10.1016/j.jmgm.2017.05.002
  8. Y. Komeiji, Y. Okiyama, Y. Mochizuki, and K. Fukuzawa “Explicit solvation of single-stranded DNA,a binding protein, and their complex: a suitable protocol for fragment molecular orbital calculation” Chem-Bio Informatics J., 17, 72-84 (2017).  https://doi.org/10.1273/cbij.17.72
  9. T. Nakano, Y. Mochidzuki, K. Fukuzawa, Y. Okiyama, and C. Watanabe “A Preliminary Study of Correction for Inter Fragment Interaction Energy (IFIE) between Fragments Sharing Bond Detached Atom (BDA)”  Journal of Computer Aided Chemistry, 18, 143-148(2017).  (https://doi.org/10.2751/jcac.18.143 In Japanese, 中野達也, 望月祐志, 福澤 薫, 沖山佳生, 渡邉千鶴「Bond detached atom (BDA)を共有しているフラグメント間の相互作用エネルギーの補正に関する試み」
  10. C. Watanabe, H. Watanabe, K. Fukuzawa, Lorien J. Parker, Y. Okiyama, H. Yuki, S. Yokoyama, H. Nakano, S. Tanaka, and T. Honma “Theoretical Analysis of Activity Cliffs among Benzofuranone-Class Pim1 Inhibitors Using the Fragment Molecular Orbital Method with Molecular Mechanics Poisson-Boltzmann Surface Area (FMO+MM-PBSA) Approach” J. Chem. Inf. Model., 57, 2996-3010 (2017). https://doi.org/10.1021/acs.jcim.7b00110
  11. I. Kobayashi, R. Takeda, R. Suzuki, K. Shimamura, H. Ishimura, R. Kadoya, K. Kawai, M. Takimoto-Kamimura, and N. Kurita “Specific interactions between androgen receptor and its ligand: ab initio molecular orbital calculations in water” J. Mol. Graph. Model., 75, 383-389 (2017). https://doi.org/10.1016/j.jmgm.2017.06.003
  12. S. Tanaka, K. Fukuzawa, and T. Honma “Large-scale data analysis accelerates FMO drug discovery” CICSJ Bull. 35, 205-209.  https://doi.org/10.11546/cicsj.35.205  In Japanese, 田中 成典, 福澤 薫, 本間 光貴「FMO創薬を加速する大規模データ解析」日本化学会情報化学部会誌.

2016

  1. M. Araki, N. Kamiya, M. Sato, M. Nakatsui, T. Hirokawa, and Y. Okuno*
    “The Effect of Conformational Flexibility on Binding Free Energy Estimation between Kinases and Their Inhibitors” J. Chem. Inf. Model., 56, 2445–2456 (2016). https://doi.org/10.1021/acs.jcim.6b00398

Books

2021

  1. Y. Mochizuki, S.Tanaka and K. Fukuzawa “Recent Advances of the Fragment Molecular Orbital Method” Springer Nature, (2021). https://doi.org/10.1007/978-981-15-9235-5

2020年

  1. Y.Okiyama, K.Fukuzawa, Y.Komeiji, and S.Tanaka ”Taking Water into Account with the Fragment Molecular Orbital Method” in : Alexander Heifetz (ed.) ”Quantum Mechanics in Drug Discovery”   Humana Press, (2020). https://doi.org/10.1007/978-1-0716-0282-9_7