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.
Referencesedit
^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. PMC5734301. 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. PMC56910. 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. PMC441519. 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. PMC1933214. PMID 17488841.
apbs, software, apbs, previously, also, advanced, poisson, boltzmann, solver, free, open, source, software, solving, equations, continuum, electrostatics, intended, primarily, large, biomolecular, systems, available, under, license, apbs, pdb2pqroriginal, auth. 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 APBS and PDB2PQROriginal 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 Repositorygithub wbr com wbr Electrostatics wbr apbs pdb2pqrWritten inPython C COperating systemLinuxTypeMolecular electrostaticsLicense license Websitewww wbr poissonboltzmann wbr orgPDB2PQR 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 edit 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 editOfficial website Official documentation APBS PDB2PQR and related software GitHub nbsp This article about molecular modelling software is a stub You can help Wikipedia by expanding it vte Retrieved from https en wikipedia org w index php title APBS software amp oldid 1191131367, wikipedia, wiki, book, books, library,
