Differences between revisions 2 and 3

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
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
hide uninteresting structures	under tree model window, select water chain substructure and delete it
	rotate structure by mouse drag	shows how it is bound together
show surfaces of the protein	select a leaf on the tree, then right click -> depict -> surface	shows how parts of protein bind
explore interaction between tp53 and brca1

Data Files: Attach data files

Presentation: Attach your presentation

Webstart: Attach a webstart

Video: Attach a video link

-  ← Revision 2 as of 2008-08-13 18:51:03 →
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+  ← Revision 3 as of 2008-08-13 18:55:08 →
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+|| hide uninteresting structures  || under tree model window, select water chain substructure and delete it ||  ||

||  || rotate structure by mouse drag || shows how it is bound together ||

|| show surfaces of the protein || select a leaf on the tree, then right click -> depict -> surface || shows how parts of protein bind ||

|| explore interaction between tp53 and brca1 ||  ||  ||

Diff for "StructureVizRecipe"

Structure Visualization with Chimera and Structure Function Linkage Database