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Appion specifications

Information


Unique identifier OMICS_15599
Name Appion
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Database management system MySQL
License Apache License version 2.0
Computer skills Medium
Version 3.3
Stability Stable
Source code URL http://emg.nysbc.org/redmine/projects/appion/files
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Gabriel Lander

Publications for Appion

Appion citations

 (100)
library_books

Structure of a cleavage independent HIV Env recapitulates the glycoprotein architecture of the native cleaved trimer

2018
Nat Commun
PMCID: 5955915
PMID: 29769533
DOI: 10.1038/s41467-018-04272-y

[…] All of the collected frames were aligned prior to processing. CTF estimation was carried out using CTFFind3, and particles were picked using an automated particle-picking program implemented in the Appion software package. Particles were stacked using a box size of 256 × 256 pixels at 1.31 Å/pix in EMAN boxer.py via Appion. Three rounds of reference-free 2D classification were carried out using […]

call_split

Glycosylation of Human IgA Directly Inhibits Influenza A and Other Sialic Acid Binding Viruses

2018
Cell Rep
PMCID: 5905402
PMID: 29617676
DOI: 10.1016/j.celrep.2018.03.027
call_split See protocol

[…] e acquisition software Leginon (), and images were acquired on a Tietz 4k CMOS detector at a magnification of 52,000× and a final pixel size of 2.05 Ǻ. Raw images were automatically uploaded into the Appion database (). Particles were individually picked from raw images using DoG Picker (), placed into a stack, and binned by 2. Reference-free two-dimensional classification was done using multi-ref […]

call_split

Cryo electron microscopy structure of a human PRMT5:MEP50 complex

2018
PLoS One
PMCID: 5843215
PMID: 29518110
DOI: 10.1371/journal.pone.0193205
call_split See protocol

[…] equipped with a Gatan US4000 CCD camera under the control of Gatan DIGITAL MICROGRAPH software at a defocus of 1 μm.The 3D reconstruction utilized 193 cryo-EM movie stacks collected using the LEGINON/APPION interface [] to automate operation of a FEI Titan Krios microscope at 300 kV with an actual magnification of 50,000x and a pixel size of 1 Å2. Each movie stack contained 40 frames collected wit […]

call_split

Rational design of a trispecific antibody targeting the HIV 1 Env with elevated anti viral activity

2018
Nat Commun
PMCID: 5830440
PMID: 29491415
DOI: 10.1038/s41467-018-03335-4
call_split See protocol

[…] grids and stained with 2% uranyl formate. Negative stain EM images were taken on a 120 kv Tecnai Spirit microscope with a LAB6 filament. Raw micrographs were collected using Leginon and deposited in Appion. DoG picker was performed to select particles in stain. Those particles were stacked and aligned using Iterative MSA/MRA. 2D classes representing the complex are shown in Fig.  and Supplementar […]

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Initiation, extension, and termination of RNA synthesis by a paramyxovirus polymerase

2018
PLoS Pathog
PMCID: 5823471
PMID: 29425244
DOI: 10.1371/journal.ppat.1006889
call_split See protocol

[…] utomated image acquisition software package Leginon []. The images were acquired at a nominal underfocus of -0.9 μm to -1.8 μm and electron doses of ~25 e-/Å2.Image processing was performed using the Appion software package[]. Contrast transfer functions of the images were corrected using ctffind4 []. Individual particles in the 67,000× images were selected using automated picking protocols follow […]

library_books

The peroxisomal AAA ATPase Pex1/Pex6 unfolds substrates by processive threading

2018
Nat Commun
PMCID: 5762779
PMID: 29321502
DOI: 10.1038/s41467-017-02474-4

[…] electrons/Å2, and a nominal defocus range between 0.5 and 1.5 µm.A total of 1097 micrographs were collected for the complex. Initial steps of data processing and 2D analyses were performed using the Appion image processing pipeline. The contrast transfer function (CTF) of each micrograph was determined using CTFFIND v3 implemented within Appion. Particles were selected from micrographs using Diff […]

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Appion institution(s)
National Resource for Automated Molecular Microscopy, The Scripps Institute, La Jolla, CA, USA; Institute of Molecular Biophysics, Department of Chemistry and Biochemistry, Florida State University, Tallahasse, FL, USA
Appion funding source(s)
This project was primarily funded by grants from the National Institutes of Health (NIH) through the National Center for Research Resources’ P41 program (grants RR17573, RR023093), and additionally by a fellowship from the ARCS foundation.

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