Protein complex interactions

[traum...@gmail.com]

Hi, I am building a PPIN based on literature review and am unsure of the best way to represent interactions between protein complexes? Is there any literature out there on this topic? e.g. should an interaction between a protein substrate and an enzymatic protein complex have edges between the substrate and all proteins involved in the complex, or just the one containing the binding site?

Any recommendations would be greatly appreciated.

Thanks,

James

[Barry Demchak]

Hi, James --

Good question. 

Cytoscape does have a grouping facility, but it's not quite targeted to your use. 

I think you're looking for an interaction between a protein and a group, which may contain proteins or anything else, really.

We don't know of any standard models for this, and Cytoscape can't do this well ... and we don't know of any file formats that encode this.

One thing that Cytoscape can do is embed a graph into a node ... take a look at the Nested Node Format (http://wiki.cytoscape.org/Cytoscape_3/UserManual/Network_Formats#nnf) and its Cytoscape use. The down side to this is that you can't link to members in a nested network from outside of the nesting node.

Does this help??