Cytoscape Wiki
Structure Visualization with Chimera and Structure Function Linkage Database
John (Scooter) Morris
University of California, San Francisco
Biological Use Case: Identify protein-protein interactions at a deep level by examining structural information. In this case, we will look at breast cancer data.
Recipe
Cytoscape version: Version number (2.6)
Plugins to Load: Structure Visualization demo (TODO: get URL and actual name)
GUI steps:
Describe each step (story), the GUI action to take, and probable remarks
Story |
Action |
Remarks |
look at breast cancer data and human interactome network |
open human.cys |
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explore structural information for 'hub' gene tp53 |
right-click on tp53 node. Select view structure -> 1tup from popup menu. |
this will bring up chimera and show co-crystal structure of p53 trimer bound to DNA |
show secondary structure |
use preset of ribbons |
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