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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. 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).
  • 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).
  • K. Chiba, T. Hirano, F. Sato, M. Okamoto, “A Density Functional Study on Reaction Center Models of Horse Heart Carbonmonoxy Myoglobin –Effect of Distal Histidine to the Electronic States–”, J. Comput. Chem., Jpn, 7, 165-170 (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).
  • 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. 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).

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.