NetworkView

The NetworkView plugin allows the user to study allostery and signaling through network models. It can be used to display and manipulate representations of the networks projected onto the underlying molecular structures. Networks stored in simple formats can be loaded and mapped onto molecular structures.

The Luthey-Schulten Group has developed a detailed tutorial that demonstrates the use of the NetworkView plugin.

Please go to the following URL and download the tutorial near the bottom of the page entitled: Dynamical Network Analysis.

http://faculty.scs.illinois.edu/schulten/tutorials/

The simplest networks consist of sets of nodes and edges that connect pairs of nodes. For example, in protein·protein interaction networks, nodes represent individual proteins, and if two proteins interact with one another, an edge is drawn between their nodes.

Dynamical Network Representations

The NetworkView plugin can display dynamical network representations by loading a network file via File | Load Network.... Once the network is loaded, you can choose to perform "Action"s on the network (or subnetworks, defined by the choices made in the Node Selection section of the plugin), listed in the box at the bottom of the plugin window. Chose your desired action and then click Apply. You can perform multiple Actions, and when you want to actually view the results, click the Draw button at the bottom of the plugin window.

Communities

Community Data can be loaded into the NetworkView plugin by selecting File | Load Community Data.... You can then use the Node Selection section of the plugin to choose individual communities to perform Actions upon.

Critical nodes between communities can be displayed by choosing the proper Node Selection.

Optimal and Suboptimal Paths

Optimal and Suboptimal paths can be loaded into the plugin and mapped onto molecular structures. You can choose to view all paths, or specific paths via the Node Selection.

Advanced Features

Via TCL scripting, you can perform more complex operations than are exposed via the plugin window. See the tutorial for additional information on e.g., retrieving specific information about edges that connect subnetworks and other metrics.