APBS specifications

Information


Unique identifier OMICS_20482
Name APBS
Interface Web user interface
Restrictions to use None
License BSD 3-clause “New” or “Revised” License, MIT License
Computer skills Basic
Maintained No

Documentation


Maintainers


This tool is not maintained anymore.

Additional information


http://apbs-pdb2pqr.readthedocs.io/en/latest/

Information


Unique identifier OMICS_20482
Name APBS
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++, Javascript, MATLAB, Python
License BSD 3-clause “New” or “Revised” License, MIT License
Computer skills Advanced
Version 1.5
Stability Stable
Source code URL https://codeload.github.com/Electrostatics/apbs-pdb2pqr/zip/apbs-1.5
Registration required Yes
Maintained Yes

Download


Versioning


Add your version

Documentation


Maintainers


  • person_outline Nathan Baker <>
  • person_outline Robert Hanson <>
  • person_outline Malcolm Tobias <>
  • person_outline Sriram Krishnan <>

Additional information


http://apbs-pdb2pqr.readthedocs.io/en/latest/

Publication for APBS

APBS in publications

 (14)
PMCID: 5871869
PMID: 29593217
DOI: 10.1038/s41467-018-03632-y

[…] structure with glycans omitted as a search model., superposition and figures were rendered using pymol (version 1.5.0.4 schrodinger, llc), and protein electrostatic calculations were achieved using apbs and pdb2pqr webservers. bsas were determined with pdbepisa using a 1.4-å probe. potential hydrogen bonds were assigned using a distance of <3.6 å and an a-d-h angle of >90°, […]

PMCID: 5903867
PMID: 29661272
DOI: 10.7554/eLife.35419.035

[…] pymol (the pymol molecular graphics system, schrödinger, llc), and those in , and were prepared with ucsf chimera (). electrostatic distributions were calculated using pdb2pqr and displayed using apbs ()., the lipid mixture of dopg, dopc and dope at a molar ratio 2:3:5 () was spread over a 200 μm diameter hole in a 0.5 mm thick teflon sheet partition. a planar lipid bilayer formed at the hole […]

PMCID: 5777263
PMID: 29183996
DOI: 10.1074/jbc.M117.815258

[…] 5ovt (td-bph:epoxomicin), and 5ovu (cm-bph). structures were visualized using pymol v1.8.0.5, and electrostatic potentials were calculated at ± 5 kt/e (at 298k 1kt/e equals 25.7 mv) with the apbs plugin and pdb code pdb2pqr using default settings ()., a. c. d. f., m. d. h., and j. m. designed the experiments. a. c. d. f., l. m., k. h., and m. d. h. performed the experiments. a. c. d. f., […]

PMCID: 5775413
PMID: 29095434
DOI: 10.1038/cddis.2017.563

[…] the effect of egcg on the dimerization of the lc3-i protein., the molecular dynamic (md) simulations were conducted with the software package gromacs version 4.6.7. the protein esp was depicted with apbs server. chimera program was used for trajectory visualization and analysis. the gromos96 53a6 force field was used for proteins. the force field parameters for egcg were adopted from a previous […]

PMCID: 5571608
PMID: 28836963
DOI: 10.1186/s12864-017-4045-3

[…] as described above. electrostatic potential on the solvent accessible surfaces of the proteins were calculated using pdb2pqr [] (in the amber force field) and adaptive poisson-boltzmann solver (apbs) []. the head-to-head dimers were randomly selected from both the active and the inactive hexamers of the protein for performing md simulations, to save computational time. various energy […]


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APBS institution(s)
Center for Computational Biology, Washington University in St. Louis, MO, USA; Center for Computational Biology, Washington University in St. Louis, MO, USA; Department of Chemistry, St. Olaf College, MN, USA; Center for Computational Biology, Washington University in St. Louis, MO, USA; National Biomedical Computation Resource, University of California San Diego, CA, USA; National Biomedical Computation Resource, University of California San Diego, CA, USA; School of Biomolecular and Biomedical Science, University College Dublin, Ireland
APBS funding source(s)
Supported by NIH award P41 RR00860516 to the National Biomedical Computation Resource; NIH grants R01 GM069702 and 3R01 GM069702-06S1 (ARRA administrative supplement) to NAB.

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