UCSF structureViz

Category Proteomics>Protein Structure/Modeling Systems/Tools

Abstract UCSF structureViz is a Cytoscape plug-in that links the visualization of biological networks (and biological relationships expressed as networks) provided by Cytoscape with the visualization and analysis of macromolecular structures and sequences provided by UCSF Chimera.

It is part of a broader effort to develop and apply tools for the visualization and analysis of biological context (see below...).

structureViz provides commands to open structures in UCSF Chimera, align open structures using Chimera's Sequence/Structure tools, and exit Chimera.

In order to load a structure associated with a node, the Protein Data Bank (PDB) identifier (or identifiers, if there are more than one) must be present as an attribute of that node.

Currently, structureViz will look for an attribute named Structure, pdb, or pdbFileName. When a structure is opened, structureViz provides an alternative interface to Chimera: the Cytoscape Molecular Structure Navigator.

This interface uses a tree-based paradigm to allow users to select and affect the display of models, chains, and residues, mostly through the use of context menus.

Additional commands allow for selection by chemistry (Ligand, Ions, Solvent, Secondary Structure, and in the model context menu, Functional Residues). Users can also take advantage of Chimera’s structural alignment capabilities by using the “Align” command.

Furthermore, structureViz is an analysis tool to provide a bridge between the broad context of the systems biologist and the detailed, molecular understanding of the molecular or structural biologist (see below...).

structureViz as a plug-in to Cytoscape --

structureViz is a plug-in to Cytoscape (as stated above...), an open source network visualization application used to explore biological networks of various kinds and, more recently, protein similarity networks.

Cytoscape provides a broad context for exploring [sequence-->structure-->function] relationships. Cytoscape provides an excellent plug-in mechanism that will allow you to extend its functionality to meet your needs.

Examples of Cytoscape plug-ins include BiNGO, which maps Gene Ontology (GO) information to Cytoscape nodes;

cPath, which allows users to query retrieve and visualize data from the cancer pathway (cPath) database; and the PhenoType Genetics plug-in (see below...), which constructs genetic-interaction networks from large sets of phenotype measurements.

PhenoType Genetics plug-in - Constructs genetic-interaction networks from large sets of phenotype measurements from cells with single and pairwise genetic perturbations. Network derivation is generalized and fully computable.

It also implements network-analysis methods to find local and global interaction patterns reflecting the effects of gene perturbations on biological processes and pathways.

structureViz Description --

structureViz allows Cytoscape users to select nodes representing proteins in their biological networks and interactively display and analyze the 3D structures associated with those proteins in UCSF Chimera.

Users can associate structures from the PDB with their sequences by National Center for Biotechnology Information (NCBI) GI number using a Cytoscape node attribute file provided on the Resource for Biocomputing, Visualization and Informatics (RBVI) website (see below...).

Alternatively, users can provide their own data by annotating their nodes with any one of the following attributes: pdb, pdbFileName or structure (as stated above...). The values of these attributes should be comma-separated lists of PDB identifiers.

Once this association is made, structureViz can be used to open the structure(s) in Chimera, perform structural analyses (e.g. compare structures), and if desired, augment the Cytoscape network with the results of the comparisons.

structureViz Significance --

structureViz, along with the node annotation file, provide important tools for both the systems biologist and the structural biologist. With structureViz, multiple levels of abstracted biological data are integrated into a single interface for visualization and analysis.

This takes advantage of two (2) advanced, yet typically disparate fields of study: structural biology and systems biology, and hence can inspire new ways of thinking about biology.

The systems biologist is now able to much more easily explore the possible structural implications of protein-protein partners, or neighbors in a metabolic pathway.

structureViz also provides an important ability to explore the possible functional and evolutionary significance of sequence relationships between proteins.

For the structural biologist, structureViz, along with Cytoscape can provide useful information that can suggest targets for experimental verification of structural relationships, or targets for solving the structure through nuclear magnetic resonance (NMR), crystallography, or modeling.

The Resource for Biocomputing, Visualization and Informatics (RBVI) website provides additional Cytoscape Plug-ins developed or supported by the UCSF RBVI --

1) ShortestPath - Find the shortest weighted path between any two nodes -

ShortestPath is a plug-in for Cytoscape that can be used to show the shortest weighted path between two (2) selected nodes in the current network. It is based on the ShortestPath plug-in developed by Marcio Rosa da Silva.

ShortestPath supports the use of edge attributes to calculate the path lengths. It supports both directed and undirected networks and it gives the user the possibility to choose which node (of the selected ones) should be used as source and target (useful for directed networks).

The plug-in Application Programming Interface (API) makes it possible to use its functionality from another plug-in.

2) Metanodes Plug-in -

The Metanodes Plug-in is a Cytoscape Plug-in that provides a dialog that allows users to select a group of nodes in a network and create a metanode that represents them. (metanode - A metanode is a graph node that represents a sub-graph that is at a lower level of abstraction).

This metanode can be “collapsed” and “expanded”. New metanodes can contain child networks that are composed of metanodes, thus creating a hierarchical structure in the network.

The Plug-in transfer’s node attributes to the new metanode by doing a performing operation on its children nodes.

3) Edge-weighted layout -

The Edge-weighted layout is a layout plug-in based on the Fruchterman-Reingold and Kamada-Kawai algorithms, but modified to utilize a user-specified edge attribute as a weighting value to compute the attractive forces of an edge.

This work (software) has now been integrated into the Cytoscape core plug-in AutomaticLayout.jar.

4) clusterMaker: Creating and Visualizing Cytoscape Clusters -

UCSF clusterMaker is a Cytoscape plug-in that unifies different clustering techniques and displays into a single interface.

Current clustering algorithms include Hierarchical and k-Means for clustering expression or genetic data, and MCL and FORCE for clustering similarity networks to look for protein families (and putative functional similarities).

Hierarchical and k-Means clusters may be displayed as hierarchical groups of nodes or as heat maps.

MCL and FORCE both create collapsible “meta nodes” to allow interactive exploration of the putative family associations within the Cytoscape network, and MCL results may also be shown as a separate network containing only the intra-cluster edges.

5) UCSF clusterExplorer -

UCSF clusterExplorer is a Cytoscape plug-in that provides a number of tools for exploring clusters created by Cytoscape clustering tools such as clusterMaker.

clusterExplorer also provides a number of tools to view information about the cluster sizes, inter and intra cluster edge weights, and five (5) comparative methods to delve into specific features of nodes and clusters with respect to other nodes and clusters.

System Requirements

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Manufacturer Web Site UCSF structureViz

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G6G Abstract Number 20709

G6G Manufacturer Number 104281