Citing your use of our software — APBS-PDB2PQR 1.6 documentation

# Citing your use of our software

Please acknowledge your us of our software by citing:

> - Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, Brookes DH, Wilson L, Chen J, Liles K, Chun M, Li P, Gohara DW, Dolinsky T, Konecny R, Koes DR, Nielsen JE, Head-Gordon T, Geng W, Krasny R, Wei GW, Holst MJ, McCammon JA, Baker NA. Improvements to the APBS biomolecular solvation software suite. Protein Science, 27, 112-128, 2018. http://dx.doi.org/10.1002/pro.3280

You may also wish to include one or more of the following citations:

- Original PDB2PQR citations
  - Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res, 35, W522-5, 2007. http://nar.oxfordjournals.org/content/35/suppl_2/W522
  - Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res, 32, W665-W667, 2004. http://nar.oxfordjournals.org/content/32/suppl_2/W665.abstract
- Original APBS citation
  - Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. http://www.pnas.org/content/98/18/10037
  - Additional articles discussing APBS and the PBE are available from the [suggested reading]
- Please acknowledge your use of PEOE_PB protein/ligand parameterization software by citing:
  - Czodrowski P, Dramburg I, Sotriffer CA, Klebe G. Development, validation, and application of adapted PEOE charges to estimate pKa values of functional groups in protein-ligand complexes. Proteins, 65, 424-437, 2006. http://onlinelibrary.wiley.com/doi/10.1002/prot.21110/abstract
- Please acknowledge your use of the Holst group software by citing:
  - For the multigrid solver:
    - 13. Holst and F. Saied, Multigrid solution of the Poisson-Boltzmann equation. J. Comput. Chem. 14, 105-113, 1993.
    - 13. Holst and F. Saied, Numerical solution of the nonlinear Poisson-Boltzmann equation: Developing more robust and efficient methods. J. Comput. Chem. 16, 337-364, 1995.
  - For the finite element solver:
    - 13. Holst, Adaptive numerical treatment of elliptic systems on manifolds. Advances in Computational Mathematics 15, 139-191, 2001 http://dx.doi.org/10.1023/A:1014246117321
    - 18. Bank and M. Holst, A New Paradigm for Parallel Adaptive Meshing Algorithms. SIAM Review 45, 291-323, 2003. http://epubs.siam.org/doi/abs/10.1137/S003614450342061