APBS (software)

APBS and PDB2PQR
Original author(s)	Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (APBS); Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA (PDB2PQR)
Repository	github.com/Electrostatics/apbs-pdb2pqr
Written in	Python, C++, C
Operating system	Linux
Type	Molecular electrostatics
Website	www.poissonboltzmann.org

APBS (previously also Advanced Poisson-Boltzmann Solver) is a free and open-source software for solving the equations of continuum electrostatics intended primarily for the large biomolecular systems.^[1]^[2] It is available under the BSD license.

PDB2PQR prepares the protein structure files from Protein Data Bank for use with APBS. The preparation steps include, but aren't limited to adding missing heavy atoms to the structures and assigning charges from a number of force fields.^[3]^[4] The output file format is PQR^[5] and that's where the name of the software comes from.

References

^ Jurrus, Elizabeth; Engel, Dave; Star, Keith; Monson, Kyle; Brandi, Juan; Felberg, Lisa E.; Brookes, David H.; Wilson, Leighton; Chen, Jiahui (2017-08-24). "Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite". Protein Science. 27 (1): 112–128. doi:10.1002/pro.3280. PMC 5734301. PMID 28836357.
^ McCammon, J. Andrew; Holst, Michael J.; Joseph, Simpson; Sept, David; Baker, Nathan A. (2001-08-28). "Electrostatics of nanosystems: Application to microtubules and the ribosome". Proceedings of the National Academy of Sciences. 98 (18): 10037–10041. Bibcode:2001PNAS...9810037B. doi:10.1073/pnas.181342398. ISSN 0027-8424. PMC 56910. PMID 11517324.
^ Baker, Nathan A.; McCammon, J. Andrew; Nielsen, Jens E.; Dolinsky, Todd J. (2004-07-01). "PDB2PQR: an automated pipeline for the setup of Poisson–Boltzmann electrostatics calculations". Nucleic Acids Research. 32 (suppl_2): W665–W667. doi:10.1093/nar/gkh381. ISSN 0305-1048. PMC 441519. PMID 15215472.
^ Baker, Nathan A.; Klebe, Gerhard; Jensen, Jan H.; Nielsen, Jens E.; Li, Hui; Czodrowski, Paul; Dolinsky, Todd J. (2007-07-01). "PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations". Nucleic Acids Research. 35 (suppl_2): W522–W525. doi:10.1093/nar/gkm276. ISSN 0305-1048. PMC 1933214. PMID 17488841.
^ "PQR molecular structure format — APBS-PDB2PQR 1.6 documentation". apbs-pdb2pqr.readthedocs.io. Retrieved 2019-05-23.

External links

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[1] Jurrus, Elizabeth; Engel, Dave; Star, Keith; Monson, Kyle; Brandi, Juan; Felberg, Lisa E.; Brookes, David H.; Wilson, Leighton; Chen, Jiahui (2017-08-24). "Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite". Protein Science. 27 (1): 112–128. doi:10.1002/pro.3280. PMC 5734301. PMID 28836357.

[2] McCammon, J. Andrew; Holst, Michael J.; Joseph, Simpson; Sept, David; Baker, Nathan A. (2001-08-28). "Electrostatics of nanosystems: Application to microtubules and the ribosome". Proceedings of the National Academy of Sciences. 98 (18): 10037–10041. Bibcode:2001PNAS...9810037B. doi:10.1073/pnas.181342398. ISSN 0027-8424. PMC 56910. PMID 11517324.

[3] Baker, Nathan A.; McCammon, J. Andrew; Nielsen, Jens E.; Dolinsky, Todd J. (2004-07-01). "PDB2PQR: an automated pipeline for the setup of Poisson–Boltzmann electrostatics calculations". Nucleic Acids Research. 32 (suppl_2): W665–W667. doi:10.1093/nar/gkh381. ISSN 0305-1048. PMC 441519. PMID 15215472.

[4] Baker, Nathan A.; Klebe, Gerhard; Jensen, Jan H.; Nielsen, Jens E.; Li, Hui; Czodrowski, Paul; Dolinsky, Todd J. (2007-07-01). "PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations". Nucleic Acids Research. 35 (suppl_2): W522–W525. doi:10.1093/nar/gkm276. ISSN 0305-1048. PMC 1933214. PMID 17488841.

[5] "PQR molecular structure format — APBS-PDB2PQR 1.6 documentation". apbs-pdb2pqr.readthedocs.io. Retrieved 2019-05-23.

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