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📚 論文 & 引用 (Publications & Citations)

学術研究等で ProteinDF または QCLO 法をご利用いただいた際は、以下の原著論文を引用してください。

🎯 原著論文（Primary Citations）

ProteinDF プログラム開発論文

  1. Development of a new density functional program for all-electron calculation of proteins
    F. Sato, Y. Shigemitsu, I. Okazaki, S. Yahiro, M. Fukue, S. Kozuru, H. Kashiwagi
    Int. J. Quant. Chem., 63, 245–246 (1997).
    DOI: 10.1002/(SICI)1097-461X(1997)63:1<245::AID-QUA27>3.0.CO;2-9
📋 BibTeX を表示 
@article{sato1997development,
  title={Development of a new density functional program for all-electron calculation of proteins},
  author={Sato, F and Shigemitsu, Y and Okazaki, I and Yahiro, S and Fukue, M and Kozuru, S and Kashiwagi, H},
  journal={International journal of quantum chemistry},
  volume={63},
  number={1},
  pages={245--246},
  year={1997},
  publisher={Wiley Online Library}
}
  1. Development of a restricted open shell Kohn–Sham program and its application to a model heme complex
    I. Okazaki, F. Sato, T. Yoshihiro, T. Ueno, H. Kashiwagi
    THEOCHEM, 451, 109–119 (1998).
    DOI: 10.1016/S0166-1280(98)00192-3
📋 BibTeX を表示 
@article{okazaki1998development,
  title={Development of a restricted open shell Kohn--Sham program and its application to a model heme complex},
  author={Okazaki, I and Sato, F and Yoshihiro, T and Ueno, T and Kashiwagi, H},
  journal={Journal of Molecular Structure: THEOCHEM},
  volume={451},
  number={1-2},
  pages={109--119},
  year={1998},
  publisher={Elsevier}
}
  1. Distributed parallel processing by using the object-oriented technology in ProteinDF program for all-electron calculations on proteins
    T. Yoshihiro, F. Sato, H. Kashiwagi
    Chem. Phys. Lett., 346, 313–321 (2001).
    DOI: 10.1016/S0009-2614(01)00977-9
📋 BibTeX を表示 
@article{yoshihiro2001distributed,
  title={Distributed parallel processing by using the object-oriented technology in ProteinDF program for all-electron calculations on proteins},
  author={Yoshihiro, T and Sato, F and Kashiwagi, H},
  journal={Chemical physics letters},
  volume={346},
  number={3-4},
  pages={313--321},
  year={2001},
  publisher={Elsevier}
}
  1. Development of parallel density functional program using distributed matrix to calculate all-electron canonical wavefunction of large molecules
    T. Inaba, F. Sato
    J. Comput. Chem., 28, 984–995 (2007).
    DOI: 10.1002/jcc.20626
📋 BibTeX を表示 
@article{inaba2007development,
  title={Development of parallel density functional program using distributed matrix to calculate all-electron canonical wavefunction of large molecules},
  author={Inaba, T and Sato, F},
  journal={Journal of computational chemistry},
  volume={28},
  number={5},
  pages={984--995},
  year={2007},
  publisher={Wiley Online Library}
}
  1. A third-generation density-functional-theory-based method for calculating canonical molecular orbitals of large molecules
    T. Hirano, F. Sato
    Phys. Chem. Chem. Phys., 16, 14496–14503 (2014).
    DOI: 10.1039/C4CP00244F
📋 BibTeX を表示 
@article{hirano2014third,
  title={A third-generation density-functional-theory-based method for calculating canonical molecular orbitals of large molecules},
  author={Hirano, T and Sato, F},
  journal={Physical Chemistry Chemical Physics},
  volume={16},
  number={28},
  pages={14496--14503},
  year={2014},
  publisher={Royal Society of Chemistry}
}

QCLO 法（収束計算手法）

  1. Convergence process with quasi-canonical localized orbital in all-electron SCF calculation on proteins
    H. Kashiwagi, H. Iwai, K. Tokieda, M. Era, T. Sumita, T. Yoshihiro, F. Sato
    Mol. Phys., 101, 81–86 (2003).
    DOI: 10.1080/0026897021000037728
📋 BibTeX を表示 
@article{kashiwagi2003convergence,
  title={Convergence process with quasi-canonical localized orbital in all-electron SCF calculation on proteins},
  author={Kashiwagi, H and Iwai, H and Tokieda, K and Era, M and Sumita, T and Yoshihiro, T and Sato, F},
  journal={Molecular Physics},
  volume={101},
  number={1-2},
  pages={81--86},
  year={2003},
  publisher={Taylor \& Francis}
}
  1. Study of the quasicanonical localized orbital method based on protein structures
    N. Nishino-Uemura, T. Hirano, F. Sato
    J. Chem. Phys., 127, 184106 (2007).
    DOI: 10.1063/1.2796169
📋 BibTeX を表示 
@article{nishino2007study,
  title={Study of the quasicanonical localized orbital method based on protein structures},
  author={Nishino-Uemura, N and Hirano, T and Sato, F},
  journal={The Journal of Chemical Physics},
  volume={127},
  number={18},
  pages={184106},
  year={2007},
  publisher={American Institute of Physics}
}

🔬 ProteinDF を使用した研究論文リスト

ProteinDF を活用した主な研究成果の一覧です：

2020年 – 2022年

  • T. Hirano, F. Sato, “Theoretical study of the receptor-binding domain of spike protein of SARS-CoV-2 by canonical molecular orbital calculation”, AIP Conf. Proc., 2611, 020005 (2022).
  • R. Nakaoka, T. Hirano, F. Sato, “Study on mechanism of electronic states of Interferon alpha2”, 生産研究, 74, 153-159 (2022).
  • T. Wang, T. Hirano, F. Sato, “Study on the Role in the Catalytic Reaction Occurrence of the Active Site in PETase by Canonical Molecular Orbital Method”, 生産研究, 74, 161-167 (2022).
  • T. Hirano, F. Sato, “Interaction Energy Analysis Based on Canonical Kohn-Sham Molecular Orbitals Calculation of Protein”, AIP Conf. Proc., 2343, 020007 (2021).
  • D. Maeda, T. Hirano, F. Sato, “Analysis of Electronic Structure of Photoactive Yellow Protein by Canonical Molecular Orbitals Calculation”, 生産研究, 73, 157-163 (2021).
  • T. Hirano, F. Sato, “Interaction energy analysis based on canonical Kohn-Sham molecular orbital calculation of protein”, DFT2020 (2020).
  • H. Sasaki, T. Hirano, F. Sato, “Comparison of Electronic Structures between Insulin-like Growth Factor 1 and Insulin”, 生産研究, 72, 239-246 (2020).

2015年 – 2019年

  • T. Hirano, F. Sato, “Recent progress of protein canonical molecular orbital calculation by the third generation density functional method”, AIP Conf. Proc., 2186, 030009 (2019).
  • H. Eguchi, T. Hirano, F. Sato, “Study on the Cloud-like Visualization Technique of Protein Molecular Orbitals by the Rejection Method”, 生産研究, 71, 769-773 (2019).
  • T. Hirano, F. Sato, “The electronic structure of the active site in the glucose oxidase”, HPCI Research Report, 3, 11-16 (2018).
  • H. Eguchi, T. Hirano, F. Sato, “Study on the Cloud-like Visualization Model of Protein Molecule Orbitals by the Rejection Method”, J. Comput. Chem., J., 17, 189-192 (2018).
  • T. Hirano, F. Sato, “Study of High-Performance Canonical Molecular Orbitals Calculation for Proteins”, AIP Conf. Proc., 1906, 030019 (2017).
  • S. Kihira, T. Hirano, F. Sato, “Study on Stable Structures of Oxytocin by Full-Quantum Chemical Calculation”, 生産研究, 68, 219-223 (2016).
  • T. Kim, T. Hirano, F. Sato, “Development of atomic charges for proteins by using the linear regression method based on canonical molecular orbital calculation”, 生産研究, 68, 213-217 (2016).
  • J. Yoshida, T. Hirano, F. Sato, “Electronic state calculation of the active center of Glucose Oxidase by QCLO method”, 生産研究, 67(3), 265-272 (2015).

2005年 – 2014年

  • H. Higuchi, T. Hirano, F. Sato, “Study of Practical Approach for Grid-free XC Computational Method”, 生産研究, 66, 273 (2014).
  • K. Chiba, T. Hirano, F. Sato, M. Okamoto, “Clarification of the role of protein in carbonmonoxy myoglobin by investigating electronic states”, Int. J. Quant. Chem., 113, 2345-2354 (2013).
  • T. Shimomukai, K. Chiba, J. Matsuda, T. Hirano, F. Sato, “All-Electron Wave Functions and the Density-of-States Analyses of Proteins”, J. Vis. Soc. Jpn., 32, 132-137 (2013).
  • Y. Tokita, S. Yamada, W. Luo, Y. Goto, N. Bouley-Ford, H. Nakajima, Y. Watanabe, “Protein photoconductors and photodiodes”, Angew. Chem., 50, 11663-6 (2011).
  • T. Hirano, K. Chiba, F. Sato, “ProteinDF: An All-electron Density Functional Program Package for Proteins”, Trans. Jpn. Soc. Sim. Tech., 4, 50-59 (2009).
  • Y. Tokita, J. Shimura, H. Nakajima, “Mechanism of Intramolecular Electron Transfer in the Photoexcited Zn-Substituted Cytochrome c: Theoretical and Experimental Perspective”, J. Am. Chem. Soc., 130, 5302–5310 (2008).
  • T. Inaba, N. Tsunekawa, T. Hirano, T. Yoshihiro, H. Kashiwagi, F. Sato, “Density functional calculation of the electronic structure on insulin hexamer”, Chem. Phys. Lett., 434, 331-335 (2007).
  • T. Inaba, S. Tahara, N. Nisikawa, H. Kashiwagi, F. Sato, “All-electron density functional calculation on insulin with quasi-canonical localized orbitals”, J. Comput. Chem., 26, 987-93 (2005).