Avogadro specifications

Information


Unique identifier OMICS_04967
Name Avogadro
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Avogadro_(software)

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Maintainer


  • person_outline Marcus D Hanwell <>

Publication for Avogadro

Avogadro in publications

 (48)
PMCID: 5902622
PMID: 29662099
DOI: 10.1038/s41598-018-24478-w

[…] each subunit contains two ca2+ ion binding sites, and the secondary structures are mostly α-helices., the three-dimensional model of atrazine and the energy minimization of the structure was made by avogadro (v1.1.1). the docking procedure was carried out with the dockingserver web-based application, and the results were analyzed with autodocktools (v1.5.6). the applied enzyme structure […]

PMCID: 5902962
PMID: 29692986
DOI: 10.3389/fchem.2018.00101

[…] performed by autodock vina (trott and olson, ; http://vina.scripps.edu). chemical structures were drawn by perkinelmer chembiodraw ultra (http://www.cambridgesoft.com). for ligand preparation the avogadro (hanwell et al., ; https://avogadro.cc/) software package was used. a syn-cdp toppar stream file was generated by charmm general force field program version 1.0.0 for use with cgenff version […]

PMCID: 5876379
PMID: 29599490
DOI: 10.1038/s41598-018-23624-8

[…] two butyrate carbon atoms were resolved in addition to the trehalose moiety. crystal water and ca2+ ions bound to this chain were kept. we constructed structures for the different fatty acids using avogadro 1.1 and converted them to amber prep files with antechamber. they were assigned glycam06j-1 atom types. charges were determined by performing a resp/esp fit with the resp/esp charge derive […]

PMCID: 5923396
PMID: 29597332
DOI: 10.3390/md16040109

[…] californica muscle-type nachr were obtained via the swiss model web service []. the acetylcholine structure was downloaded from the zinc database []. the makaluvamine g structure was constructed in avogadro [] and partial charges were assigned to the atoms in ucsf chimera via theam-bcc1 forcefield plugin []., cell cultures and transfection. mouse neuroblastoma neuro2a cells or sh-ep cells […]

PMCID: 5783936
PMID: 29367659
DOI: 10.1038/s41467-017-02545-6

[…] equilibrium simulations were run to assess the secondary-structural behaviour of the flag peptide, each using different starting structures. the peptide starting coordinates were generated using avogadro software as either fully linear or alpha-helix. these structures were solvated with tip3p water using the vmd solvate plugin, with box sizes 14 angstrom larger than the peptide’s longest […]


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Avogadro institution(s)
Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA

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