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Journal articles

2024

    1. Y. Handa, K. Okuwaki, Y. Kawashima, R. Hatada, Y. Mochizuki, Y. Komeiji, S. Tanaka, T. Furuishi, E. Yonemochi, T. Honma, K. Fukuzawa “Prediction of Binding Pose and Affinity of Nelfinavir, a SARS-CoV-2 Main Protease Repositioned Drug by Combining Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations” J. Phys. Chem. B128, 2249-2265 (2024). https://doi.org/10.1021/acs.jpcb.3c05564
    2. Y. Seki, C. Watanabe, N. Tani, K. Kamisaka, T. Ohyama, D. Takaya, T. Honma “Structural Stability and Binding Ability of SARS-CoV-2 Main Protease with GC376: A Stereoisomeric Covalent Ligand Analysis by FMO calculation” Chem-Bio Informatics., 24, 13-24 (2024). https://doi.org/10.1273/cbij.24.13
    3. K. Kamisaka, S. Nagase, C. Watanabe, D. Takaya, H. Yuki, T. Honma “Statistical analysis of interactions among amino acid residues in apo structures using fragment molecular orbital method” Chem-Bio Informatics J., 24, 25-47 (2024). https://doi.org/10.1273/cbij.24.25
    4. T. Suzuki, M. Yoshimura, M. Arai and R. Narikawa “Crucial residue for tuning thermal relaxation kinetics in the biliverdin-binding cyanobacteriochrome photoreceptor revealed by site-saturation mutagenesis.” J. Mol. Biol. 436(5), 168451 (2024). https://doi.org/10.1016/j.jmb.2024.168451

2023

  1. C. Watanabe, S. Tanaka, Y. Okiyama, H. Yuki, T. Ohyama, K. Kamisaka, D. Takaya, K. Fukuzawa and T. Honma “Quantum Chemical Interaction Analysis between SARS-CoV-2 Main Protease and Ensitrelvir Compared with Its Initial Screening Hit” J. Phys. Chem. Lett., 2023, 14(15) 3609–3620 (2023). https://doi.org/10.1021/acs.jpclett.2c03768
  2. K. Takeuchi, M. Senda, Y. Ikeda, K. Okuwaki, K. Fukuzawa, S. Nakagawa, M. Sasaki, A.T. Sasaki, and T. Senda “Functional molecular evolution of a GTP sensing kinase: PI5P4Kβ” FEBS Journal. https://doi.org/10.1111/febs.16763
  3. K. Takebe, M. Suzuki, T. Kuwada-Kusunose, S. Shirai, K. Fukuzawa, T. Takamiya, N. Uzawa, H. Iijima “Structural and Computational Analyses of the Unique Interactions of Opicapone in the Binding Pocket of Catechol O-Methyltransferase. A Crystallographic Study and Fragment Molecular Orbital Analyses” J. Chem. Info. Model., 63, 4468-4476 (2023). https://doi.org/10.1021/acs.jcim.3c00331
  4. K. Kato, A. Yamamoto, C. Watanabe, K. Fukuzawa “Application of Model Core Potentials to Zn- and Mg-containing Metalloproteins in the Fragment Molecular Orbital Method” Chem-Bio Informatics Journal, Vol.23, pp.14–25 (2023). https://doi.org/10.1273/cbij.23.14
  5. A. Shino, M. Otsu, K. Imai, K. Fukuzawa, E. C. Morishita ” Probing RNA–Small Molecule Interactions Using Biophysical and Computational Approaches” ACS Chem. Biol. (2023). https://doi.org/10.1021/acschembio.3c00287

2022

  1. K. Fukuzawa and S. Tanaka “Fragment Molecular Orbital Calculations for Biomolecules” Curr. Opin. Struct. Biol., 72, 127-134 (2022). https://doi.org/10.1016/j.sbi.2021.08.010
  2. R. Saito, K. Imai, D. Takimoto, T. Ezawa, S. Sugiyama, M. Takimoto-Kamimura, N. Kurita “Water molecule-mediated selective inhibition of bacterial zinc metalloproteinases by non-hydroxamate compounds: Ab initio molecular simulations” Journal of Molecular Graphics and Modelling, 2022, 114, 108200. https://doi.org/10.1016/j.jmgm.2022.108200
  3. T. Sengoku, M. Shiina, K. Suzuki, K. Hamada, K. Sato, A. Uchiyama, S. Kobayashi, A. Oguni, H. Itaya, K. Kasahara, H. Moriwaki, C. Watanabe, T. Honma, C. Okada, S. Baba, T. Ohta, H. Motohashi, M. Yamamoto, K. Ogata “Structural basis of transcription regulation by CNC family transcription factor, Nrf2” Nucleic Acids Research, 50(21), 12543–12557, (2022). https://doi.org/10.1093/nar/gkac1102
  4. H. Niwa, H. Watanabe, S. Sato, T. Harada, H. Watanabe, R. Tabusa, S. Fukasawa, A. Shiobara, T. Hashimoto, O. Ohno, K. Nakamura, K. Tsuganezawa, A. Tanaka, M. Shirouzu, T. Honma, K. Matsuno, T. Umehara “Structure–Activity Relationship and In Silico Evaluation of cis- and trans-PCPA-Derived Inhibitors of LSD1 and LSD2” ACS Med. Chem. Lett., 13(9), 1485–1492, 2022. https://doi.org/10.1021/acsmedchemlett.2c00294
  5. Y. Yagi, T. Kimura and M. Kamezawa “Biomolecular Chemical Simulations on Enantioselectivity and Reactivity of Lipase Enzymes to Azulene Derivatives” Nat. Prod. Commun., 17(6), 1-10 (2022). https://doi.org/10.1177/1934578X221108572
  6. K. Takaba, C. Watanabe, A. Tokuhisa, Y. Akinaga, B. Ma, R. Kanada, M. Araki, Y. Okuno, Y. Kawashima, H. Moriwaki, N. Kawashita, T. Honma, K. Fukuzawa and S. Tanaka “Protein–Ligand Binding Affinity Prediction of CDK2 Inhibitors by Dynamically Averaged FMO-based Interaction Energy” J. Comput. Chem. 43, 1362-1371 (2022). https://doi.org/10.1002/jcc.26940
  7. M. Fujii and S. Tanaka “Interspecies Comparison of Interaction Energies between Photosynthetic Protein RuBisCO and 2CABP Ligand” Int. J. Mol. Sci. 23, 11347 (2022). https://doi.org/10.3390/ijms231911347
  8. M. Fujii, C. Watanabe, K. Fukuzawa and S. Tanaka “Fragment Molecular Orbital Calculations Containing Mg2+ Ions: PPlase Domain of Cyclophilin G” Chem-Bio Inform. J. 22, 55-62 (2022). https://doi.org/10.1273/cbij.22.55
  9. C. Handa, Y. Yamazaki, S. Yonekubo, N. Furuya, T. Momose, T. Ozawa, T. Furuishi, K. Fukuzawa, and E. Yonemochi “Evaluating the correlation of binding affinities between isothermal titration calorimetry and fragment molecular orbital method of estrogen receptor beta with diarylpropionitrile (DPN) or DPN derivatives” J. Steroid Biochem. Mol. Biol. 222, 106152, (2022). https://doi.org/10.1016/j.jsbmb.2022.106152.
  10. K. Imai, D. Takimoto, R. Saito, C. Watanabe, K. Fukuzawa and N. Kurita “FMO calculations for zinc metalloprotease: Fragmentation of amino-acid residues coordinated to zinc ion” Chem-Bio Informatics Journal 22 21-25 (2022). https://doi.org/10.1273/cbij.22.21
  11. J. Shi, R. Kanoya, Y. Tani, S. Ishikawa, R. Maeda, S. Suzuki, F. Kawanami, N. Miyagawa, K. Takahashi, T. Oku, A. Yamamoto, K. Fukuzawa, M. Nakajima, T. Irimura, and N. Higashi “Sulfated Hyaluronan Binds to Heparanase and Blocks Its Enzymatic and Cellular Actions in Carcinoma Cells” Int. J. Mol. Sci., 23, 5055 (2022). https://doi.org/10.3390/ijms23095055
  12. K. Takeuchi, Y. Ikeda, M. Senda, A. Harada, K. Okuwaki, K. Fukuzawa, S. Nakagawa, H.Y. Yu, L. Nagase, M. Imai, M. Sasaki, Y.-H. Lo, D. Ito, N. Osaka, Y. Fujii, A. T. Sasaki, and T. Senda” The GTP responsiveness of PI5P4Kb evolved from a compromised trade-off between activity and specificity” Structure, 30, 1-14 (2022). https://doi.org/10.1016/j.str.2022.04.004
  13. K. Inaba, K. Ebihara, M. Senda, R. Yoshino, C. Sakuma, K. Koiwai, D. Takaya, C. Watanabe, A. Watanabe, Y. Kawashima, K. Fukuzawa, R. Imamura, H. Kojima, T. Okabe, N. Uemura, S. Kasai, H. Kanuka, T. Nishimura, K. Watanabe, H. Inoue, Y. Fujikawa, T. Honma, T. Hirokawa, T. Senda and R. Niwa “Molecular action of larvicidal flavonoids on ecdysteroidogenic glutathione S-transferase Noppera-bo in Aedes aegypti” BMC Biology, 2022, 20, 43. https://doi.org/10.1186/s12915-022-01233-2
  14. X. Ma, K. Higashi, K. Fukuzawa, K. Ueda, K. Kadota, Y. Tozuka, E. Yonemochi and K. Moribe. “Computational approach to elucidate the formation and stabilization mechanism of amorphous formulation using molecular dynamics simulation and fragment molecular orbital calculation” International Journal of Pharmaceutics, 615, 121477 (2022). https://doi.org/10.1016/j.ijpharm.2022.121477
  15. K. Okuwaki, K. Akisawa, R. Hatada, Y. Mochizuki, K. Fukuzawa, Y. Komeiji and Shigenori Tanaka “Collective residue interactions in trimer complexes of SARS-CoV-2 spike proteins analyzed by fragment molecular orbital method” Appl. Phys. Express 15, 017001 (2022). https://doi.org/10.35848/1882-0786/ac4300

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. 94, 1794-1798 (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. K. Fukuzawa, K. Kato, C. Watanabe, Y. Kawashima, Y. Handa, A. Yamamoto, K. Watanabe, T. Ohyama, K. Kamisaka, D. Takaya, T. Honma, “Special Feature of COVID-19 in FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2 Related Proteins”  J. Chem. Info. Model. 61, 4594-4612 (2021). http://dx.doi.org/10.33774/chemrxiv-2021-njqc8
  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
  10. S. Tanaka, S. Tokutomi, R. Hatada, K. Okuwaki, K. Akisawa, K. Fukuzawa, Y. Komeiji, Y. Okiyama, and Y. Mochizuki  “Dynamic Cooperativity of Ligand-Residue Interactions Evaluated with the Fragment Molecular Orbital Method”  J. Phys. Chem. B 125, 6501-6512 (2021).https://doi.org/10.1021/acs.jpcb.1c03043
  11.  R. Hatada, K. Okuwaki, K. Akisawa, Y. Mochizuki, Y. Handa, K. Fukuzawa, Y. Komeiji, Y. Okiyama, S. Tanaka  “Statistical interaction analyses between SARS-CoV-2 main protease and inhibitor N3 by combining molecular dynamics simulation and fragment molecular orbital calculation”  Appl. Phys. Express 14, 027003 – 027003 (2021).　https://doi.org/10.35848/1882-0786/abdac6

2020

  1. 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, 7, 3361-368 (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. 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

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 T‐cell receptors exhibiting different levels of cross‐reactivity”  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), in Japanese. https://doi.org/10.2477/jccj.2018-0028   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), in Japanese. https://doi.org/10.1254/fpj.149.240  
  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), in Japanese. https://doi.org/10.2751/jcac.18.143  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 (2017), in Japanese. https://doi.org/10.11546/cicsj.35.205 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

  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