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Protocols

Gorgon specifications

Information


Unique identifier OMICS_26914
Name Gorgon
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Input format MRC,CCP4,RAW,MAP,OFF,VRML,SSE,SEQ,PDB
Output format MRC,CCP4,RAW,BMP,MAP,OFF,VRML,SSE,SEQ,PDB
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Python
License Common Public License Version 1.0
Computer skills Medium
Version 2.2.0
Stability Stable
Maintained Yes

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Versioning


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Documentation


Maintainer


  • person_outline Matthew Baker

Publication for Gorgon

Gorgon citations

 (4)
library_books

EMBuilder: A Template Matching based Automatic Model building Program for High resolution Cryo Electron Microscopy Maps

2017
Sci Rep
PMCID: 5453991
PMID: 28572576
DOI: 10.1038/s41598-017-02725-w

[…] el-building method based on ROSETTA combines the sequence-derived prediction of backbone conformations and side chain information with a cryoEM potential map to build a backbone and assign sequences. Gorgon is an interactive modeling toolkit that performs de novo model building for cryoEM maps at resolutions of 3.5 to 10 Å, which combines sequence-based secondary structure prediction with feature […]

library_books

Structure and mechanism of the ATP synthase membrane motor inferred from quantitative integrative modeling

2016
PMCID: 5129741
PMID: 27821609
DOI: 10.1085/jgp.201611679

[…] Initial models of the Cα trace of either the TM4-TM5 or TM2-TM3 hairpins were generated following a protocol previously described (), using the versions of SSEHunter and SSEBuilder () implemented in Gorgon (https://gorgon.wustl.edu). The skeletonization used an algorithm described elsewhere () with a threshold of 0.1, assuming a resolution of 6.5 Å for the portion of the cryo-EM map corresponding […]

call_split

Protruding knob like proteins violate local symmetries in an icosahedral marine virus

2014
Nat Commun
PMCID: 4102127
PMID: 24985522
DOI: 10.1038/ncomms5278
call_split See protocol

[…] y as a template, a second round of segmentation, alignment and averaging resulted in a final average gp39 subunit.SSE identification was then performed on the averaged gp39 subunit using SSEHunter in Gorgon51. Five helices and two β-sheets were identified and corresponded to those found in capsid proteins of other tailed dsDNA bacteriophages, such as gp5 in HK97 (ref. ). In addition, a density ske […]

call_split

4.4 Å cryo EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus

2011
PMCID: 3173789
PMID: 21829169
DOI: 10.1038/emboj.2011.261
call_split See protocol

[…] s CHIKV homologue () (PDB ID: 3N40) as the template. The missing parts in the crystal structure (E1: residues 390–442; E2: residues 342–423) were modelled de novo by first tracing the backbones using GORGON (), with several visible side-chain densities serving as the anchor points.To model the TM helices, in particular, we generated the Cα models of two consecutive helices (residues 403–412 and 41 […]

Citations

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Gorgon institution(s)
National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA; Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO, USA
Gorgon funding source(s)
Supported by grants from NIH through the National Center for Research Resources (P41RR002250), the National Institute of General Medical Science (R01GM079429), the National Science Foundation (IIS-0705644, IIS-0705474, IIS-0705538), and a training fellowship from the Keck Center Biomedical Discovery Training Program of the Gulf Coast Consortia (NIH Grant No. 1 T90 DA022885-01).

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