Software:APBS
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| 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 |
| Written in | Python, C++, C |
| Operating system | Linux |
| Type | Molecular electrostatics |
| License | [[ license]] |
| Website | www |
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 et al. (2017-08-24). "Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite" (in en). Protein Science 27 (1): 112–128. doi:10.1002/pro.3280. 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" (in en). Proceedings of the National Academy of Sciences 98 (18): 10037–10041. doi:10.1073/pnas.181342398. ISSN 0027-8424. PMID 11517324. Bibcode: 2001PNAS...9810037B.
- ↑ 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" (in en). Nucleic Acids Research 32 (suppl_2): W665–W667. doi:10.1093/nar/gkh381. ISSN 0305-1048. 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" (in en). Nucleic Acids Research 35 (suppl_2): W522–W525. doi:10.1093/nar/gkm276. ISSN 0305-1048. PMID 17488841.
- ↑ "PQR molecular structure format — APBS-PDB2PQR 1.6 documentation". https://apbs-pdb2pqr.readthedocs.io/en/latest/formats/pqr.html.
External links
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