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. (Note: this is a first draft, just a recording of my scratch notes from going through this with scooter. Needs a lot of work, which I will do as I train myself)


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




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 NOTE: you need to modify structureViz.chimeraPath property to point to your installation of chimera. Then save human.cys so that the assignment persists.

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

right click on brca1. view structure -> 1gzh

has BRCT repeats, now we will see two structural residues

use preset of ribbons

show -> do backbone only

shows a less cluttered version of the view. We now see tandom BRCT repeats bound to a dimer. What does this mean biologically?

go into model, delete water, other garbage

take tp53 versons of both molecules and align them.

select align -> 1tup to 1gzh

Should see the BRCT repeat sitting in the middle of the DNA can we learn anything about tandem repeats bound to DNA?

select and then up-arrow, selects whole ???

find class detection

select chimera -> clash detection -> find classes

clear clashes

select chimera -> tool -> match model. choose desired chain, select 'apply'.

shows where there is inhibitory binding between tp53 and brca1

look at trends for prevalence of modeled structures

in model view, click on submodels to hightlight different structures.

can also use galfiltered.cys, which is already annotated with structure (hmlalpha2 and mcm1 both have 1Mnm structure annotations. Also can show relation to SubgeneViewer plugin

Data Files: Attach data files

Presentation: Attach your presentation

Webstart: Attach a webstart

Video: Attach a video link

StructureVizRecipe (last edited 2009-02-12 01:03:50 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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