ProteinDF

ProteinDF software package

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About

ProteinDF is a free and open source quantum chemistry calculation software package.

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GitHub Repository

ProteinDF

https://github.com/ProteinDF/ProteinDF

ProteinDF_bridge

https://github.com/ProteinDF/ProteinDF_bridge

ProteinDF_pytools

https://github.com/ProteinDF/ProteinDF_pytools

QCLObot

https://github.com/ProteinDF/QCLObot

manual

Cite

ProteinDF

  • F. Sato, Y. Shigemitsu, I. Okazaki, S. Yahiro, M. Fukue, S. Kozuru, H. Kashiwagi, “Development of a new density functional program for all-electron calculation of proteins”, Int. J. Quant. Chem., 63, 245-246 (1997).
  • I. Okazaki, F. Sato, T. Yoshihiro, T. Ueno, H. Kashiwagi, “Development of a restricted open shell Kohn–Sham program and its application to a model heme complex”, THEOCHEM, 451, 109-119 (1998).
  • T. Yoshihiro, F. Sato, H. Kashiwagi, “Distributed parallel processing by using the object-oriented technology in ProteinDF program for all-electron calculations on proteins”, Chem. Phys. Lett., 346, 313–321 (2001).
  • T. Inaba, F. Sato, “Development of parallel density functional program using distributed matrix to calculate all-electron canonical wavefunction of large molecules”, J. Comput. Chem., 28, 984–995 (2007).
  • T. Hirano, F. Sato, “A third-generation density-functional-theory-based method for calculating canonical molecular orbitals of large molecules”, PCCP, 16, 14496-14503 (2014).

QCLO

  • H. Kashiwagi, H. Iwai, K. Tokieda, M. Era, T. Sumita, T. Yoshihiro, F. Sato, “Convergence process with quasi-canonical localized orbital in all-electron SCF calculation on proteins”, Mol. Phys., 101, 81-86 (2003).
  • N. Nishino-Uemura, T. Hirano, F. Sato, “Study of the quasicanonical localized orbital method based on protein structures”, J. Chem. Phys., 127, 184106 (2007).

References using the ProteinDF

  • T.Hirano, F.Sato, “Theoretical study of the receptor-binding domain of spike protein of SARS-CoV-2 by canonical molecular orbital calculation”, AIP Conference Proceedings, 2611, 020005 (2022).
  • R.Nakaoka, T.Hirano, F.Sato, “Study on mechanism of electronic states of Interferon alpha2”, Seisan Kenkyu, 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”, Seisan Kenkyu, 74, 161-167 (2022).
  • T.Hirano, F.Sato, “Interaction Energy Analysis Based on Canonical Kohn-Sham Molecular Orbitals Calculation of Protein”, AIP Conference Proceedings, 2343, 020007 (2021).
  • D.Maeda, T.Hirano, F.Sato, “Analysis of Electronic Structure of Photoactive Yellow Protein by Canonical Molecular Orbitals Calculation”, Seisan Kenkyu, 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”, Seisan Kenkyu, 72, 239-246 (2020).
  • T.Hirano, F.Sato, “Recent progress of protein canonical molecular orbital calculation by the third generation density functional method”, AIP Conference Proceedings 2186, 030009 (2019).
  • H.Eguchi, T.Hirano, F.Sato, “Study on the Cloud-like Visualization Technique of Protein Molecular Orbitals by the Rejection Method”, Seisan Kenkyu, 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 Conference Proceedings, 1906, 030019 (2017).
  • S.Kihira, T.Hirano, F.Sato, “Study on Stable Structures of Oxytocin by Full-Quantum Chemical Calculation”, Seisan Kenkyu, 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”, Seisan Kenkyu, 68, 213-217, (2016).
  • J.Yoshida, T.Hirano, F.Sato, “Electronic state calculation of the active center of Glucose Oxidase by QCLO method”, Seisan Kenkyu, 67(3), 265-272 (2015).
  • T.Hirano, F.Sato, “A third-generation density-functional-theory-based method for calculating canonical molecular orbitals of large molecules”, Phys. Chem. Chem. Phys., 16, 14496-14503 (2014).
  • H.Higuchi, T.Hirano, F.Sato, “Study of Practical Approach for Grid-free XC Computational Method”, Seisan Kenkyu, 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).
  • T.Hirano, F.Sato, “Cholesky decomposition method for canonical molecular orbital calculations of proteins”, 31th JSST Annual Conference proc., (2012).
  • T.Kuroda, T.Hirano, F.Sato, “Study of the Electronic States of the ［Ni-Fe］ and ［Ni-Fe-Se］ Hydrogenase Active Center”, Seisan Kenkyu, 64, 345 (2012).
  • M.Hori, T.Hirano, F.Sato, “Computational Study of Key Steps of RuBisCO Carboxylase Reaction and Roles of Active-Site Residues”, Seisan Kenkyu, 64, 351 (2012).
  • T. Hirano, F. Sato, “Massively parallel computation strategies for canonical molecular orbital calculations of proteins”, 30th JSST Annual Conference proc., (2011).
  • 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)
  • K.Ishikawa, T.HIRANO, F.SATO, “Study on Model Chemistry for All-Electron Calculation of Proteins”, Seisan Kenkyu, 62, 241, (2010).
  • 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).
  • T.Hirano, F.Sato, “Recommendation of All-Electron Calculation in the Theoretical Study of Polypeptides”, 46th Japanese peptide symp. proc., (2009).
  • H.Yukawa, T.HIirano, Y.Nishimura, F.Sato, “High Performance Computing of Precise Electrostatic Potential on Proteins by GPU”, Seisan Kenkyu, 61, 103 (2009).
  • K.Chiba, T.Hirano, F.Sato, M.Okamoto, “A Density Functional Study on Reaction Center Models of Horse Carbonmonoxy Myoglobin – Effect of distal histidine to the electronic states -”, J. Comput. Chem. Jpn. (2008).
  • 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).
  • N.Nishino-Uemura, T.Hirano, F.Sato, “Study of the quasi-canonical localized orbital method based on protein structures”, J. Chem. Phys., 127, 184106 (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).

If you know the other unlisted articles using the ProteinDF, please let me know.

License

ProteinDF is licensed under the GNU GPL v3. The source code can be found on the Github.

Bugs

If you find any bugs, please let me know. And if you have a suggestion for improvement, please let me know.