chemViz2

Cheminformatics App for Cytoscape
Categories: molecular structure
UCSF chemViz2 is a Cytoscape app that extends the capabilities of Cytoscape into the domain of cheminformatics. chemViz2 displays 2D diagrams of compounds specified by InCHI or SMILES strings. chemViz2 can also calculate Tanimoto similarities of compounds and use the values to create chemical similarity networks, determine the most common substructure of a group of structures, and search the network using SMARTs searches. Part of such a network is shown above. The 2D diagrams can be presented as scalable independent windows or as part of a table also showing Cytoscape attributes and calculated compound descriptors, including number of hydrogen bond donors, number of hydrogen bond acceptors, molecular weight, ALogP, molecular refractivity, number of Rule of Five violations, and several more. Any of the calculated descriptors can be mapped onto Cytsocape attributes where they can be used by the VizMapper and saved with the session. In the network above, nodes are colored by the number of hydrogen bond acceptors and node borders are colored by the number of hydrogen bond donors.

1.1.0

Works with Cytoscape 3.2

Release Notes

This version includes ECPF4, ECPF6, FCPF4, and FCPF6 fingerprints as well as the new results panel visualization

1.0.3

Works with Cytoscape 3.1

Release Notes

Added fix to update allowable attributes when a new column is created.

1.0.2

Works with Cytoscape 3.1

Release Notes

Fix problem with using edge attributes for compounds.

1.0.1

Works with Cytoscape 3.1

Release Notes

This version improves command handling significantly. Commands now exist to paint structures on nodes, enable and disable the results panel, calculate MCSS, add columns to Cytoscape, and popup both the table and structure views.

1.0.0

Works with Cytoscape 3.0


CYTOSCAPE 3

Version 1.1.0

Released 19 Jun 2015

Works with Cytoscape 3.2

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