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Protocols

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)

Versioning


No version available

Maintainer


  • person_outline Marcus D Hanwell

Publication for Avogadro

Avogadro citations

 (99)
library_books

Aromatic Rings Commonly Used in Medicinal Chemistry: Force Fields Comparison and Interactions With Water Toward the Design of New Chemical Entities

2018
Front Pharmacol
PMCID: 5928326
PMID: 29740321
DOI: 10.3389/fphar.2018.00395

[…] Structures for these aromatic rings were built using Avogadro (Hanwell et al., ). Molecular mechanical (MM) topological parameters as bonds, angles, and Lennard-Jones parameters were taken from GROMOS53A6 (Oostenbrink et al., ). Due to the well–known go […]

library_books

Lignin peroxidase ligand access channel dysfunction in the presence of atrazine

2018
Sci Rep
PMCID: 5902622
PMID: 29662099
DOI: 10.1038/s41598-018-24478-w

[…] 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 was obtai […]

library_books

Insights Into the Bifunctional Aphidicolan 16 ß ol Synthase Through Rapid Biomolecular Modeling Approaches

2018
PMCID: 5902962
PMID: 29692986
DOI: 10.3389/fchem.2018.00101

[…] ies 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 […]

call_split

The Alexandria library, a quantum chemical database of molecular properties for force field development

2018
Sci Data
PMCID: 5892371
PMID: 29633987
DOI: 10.1038/sdata.2018.62
call_split See protocol

[…] ubChem and the ChemSpider databases for most of the molecules. The downloaded structures were checked for missing hydrogens and the presence of 3D coordinates. The rest of molecules were generated by Avogadro or Molden softwares and their structures were minimized before performing quantum calculations. Quantum chemistry calculations were performed using the Gaussian 09 and Gaussian 16 (ref. ) set […]

call_split

Interaction of Glycolipids with the Macrophage Surface Receptor Mincle – a Systematic Molecular Dynamics Study

2018
Sci Rep
PMCID: 5876379
PMID: 29599490
DOI: 10.1038/s41598-018-23624-8
call_split See protocol

[…] t 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 Se […]

library_books

Makaluvamine G from the Marine Sponge Zyzzia fuliginosa Inhibits Muscle nAChR by Binding at the Orthosteric and Allosteric Sites

2018
Mar Drugs
PMCID: 5923396
PMID: 29597332
DOI: 10.3390/md16040109

[…] o 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 were cul […]

Citations

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

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