structureViz specifications

Information


Unique identifier OMICS_15583
Name structureViz
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Stability Stable
Requirements
Cytoscape
Maintained Yes

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Documentation


Maintainer


  • person_outline John Morris <>

Publication for structureViz

structureViz in publications

 (4)
PMCID: 5772511
PMID: 29343701
DOI: 10.1038/s41598-017-19075-2

[…] the representative structure for each system (wild-type and alanine mutants) was submitted to ring server. the network was visualized and analyzed using rinalyzer and structureviz module of cytoscapev3.5.1. in protein-ligand 3d graph, nodes represented residues and edges symbolized different type of interactions such as van der waals, ionic interactions […]

PMCID: 5479843
PMID: 28638118
DOI: 10.1038/s41598-017-03323-6

[…] to calculate rotation angle of inter-domain bending. inter- and intra-domain interactions via hydrogen bonding were analysed and graphically presented using cytoscape coupled with ucsf chimera and structureviz programs., , electronic supplementary material , supplementary information accompanies this paper at doi:10.1038/s41598-017-03323-6 , publisher's note: springer nature remains […]

PMCID: 4987896
PMID: 27198219
DOI: 10.1093/nar/gkw315

[…] is straightforward to use and allows the user to visualize the network directly in the browser and node attributes as interchangeable layers. ring output is compatible with the rinalyzer () and structureviz () plugins for cytoscape (). the network can be visualized in the structure at atomic level thanks to the ring-viz utility for pymol available on the ring web server., ring generates […]

PMCID: 4155609
PMID: 25237389
DOI: 10.1186/1753-6561-8-S2-S2

[…] in particular, we want to ensure a consistent use of information mapping and similar cues over all views. all of the above is accomplished by adapting and extending our plugins rinalyzer [] and structureviz [] to integrate the freely available software tools cytoscape, ucsf chimera, and pro-origami into a prototypic implementation (figure ). download links and further documentation […]


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structureViz institution(s)
Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA; Department of Biopharmaceutical Sciences, University of California, San Francisco, CA, USA
structureViz funding source(s)
This work was supported by NIH grant P41 RR01081.

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