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.
