APBS (software)

{{Infobox software

| name = APBS and PDB2PQR

| author = 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)

| repo = {{URL|https://github.com/Electrostatics/apbs-pdb2pqr}}

| programming language = Python, C++, C

| operating system = Linux

| platform =

| genre = Molecular electrostatics

| license =

| website = {{URL|https://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.{{Cite journal|last1=Jurrus|first1=Elizabeth|last2=Engel|first2=Dave|last3=Star|first3=Keith|last4=Monson|first4=Kyle|last5=Brandi|first5=Juan|last6=Felberg|first6=Lisa E.|last7=Brookes|first7=David H.|last8=Wilson|first8=Leighton|last9=Chen|first9=Jiahui|date=2017-08-24|title=Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite|journal=Protein Science|language=en|volume=27|issue=1|pages=112–128|doi=10.1002/pro.3280|pmc=5734301|pmid=28836357}}{{Cite journal|last1=McCammon|first1=J. Andrew|last2=Holst|first2=Michael J.|last3=Joseph|first3=Simpson|last4=Sept|first4=David|last5=Baker|first5=Nathan A.|date=2001-08-28|title=Electrostatics of nanosystems: Application to microtubules and the ribosome|journal=Proceedings of the National Academy of Sciences|language=en|volume=98|issue=18|pages=10037–10041|doi=10.1073/pnas.181342398|issn=0027-8424|pmid=11517324|pmc=56910|bibcode=2001PNAS...9810037B|doi-access=free}} 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.{{Cite journal|last1=Baker|first1=Nathan A.|last2=McCammon|first2=J. Andrew|last3=Nielsen|first3=Jens E.|last4=Dolinsky|first4=Todd J.|date=2004-07-01|title=PDB2PQR: an automated pipeline for the setup of Poisson–Boltzmann electrostatics calculations|journal=Nucleic Acids Research|language=en|volume=32|issue=suppl_2|pages=W665–W667|doi=10.1093/nar/gkh381|pmid=15215472|issn=0305-1048|pmc=441519}}{{Cite journal|last1=Baker|first1=Nathan A.|last2=Klebe|first2=Gerhard|last3=Jensen|first3=Jan H.|last4=Nielsen|first4=Jens E.|last5=Li|first5=Hui|last6=Czodrowski|first6=Paul|last7=Dolinsky|first7=Todd J.|date=2007-07-01|title=PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations|journal=Nucleic Acids Research|language=en|volume=35|issue=suppl_2|pages=W522–W525|doi=10.1093/nar/gkm276|pmid=17488841|issn=0305-1048|pmc=1933214}} The output file format is PQR{{Cite web|url=https://apbs-pdb2pqr.readthedocs.io/en/latest/formats/pqr.html|title=PQR molecular structure format — APBS-PDB2PQR 1.6 documentation|website=apbs-pdb2pqr.readthedocs.io|access-date=2019-05-23}} and that's where the name of the software comes from.