UCSF structureViz is a Cytoscape plugin that links visualization of biological networks in Cytoscape with visualization and analysis of molecular structures in UCSF Chimera. It is part of a broader effort to develop and apply tools for the visualization and analysis of biological context.
Networks have nodes and edges. For structureViz, molecular structures are associated with nodes using the node attributes. Macromolecular structures are specified by Protein Data Bank identifiers (PDB IDs) and small molecule structures by SMILES strings. Homology-modeled protein structures can also be associated, as detailed below.
As an alternative to interacting with Chimera directly, structureViz provides a simplified, tree-based interface to structures called the Cytoscape Molecular Structure Navigator. This interface allows selecting models, chains, and residues and adjusting their display. Basic interfaces are also provided for spatially aligning macromolecular structures and for analyzing steric clashes and hydrogen bonds.
***New version coming with Cytoscape 3.1***