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| '''__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. | '''__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) |
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|| explore interaction between tp53 and brca1 || || || || || || || |
|| 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 background 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 || || |
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)
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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hide uninteresting structures |
under tree model window, select water chain substructure and delete it |
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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 |
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use preset of ribbons |
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show -> do background 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 |
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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? |
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select and then up-arrow, selects whole ??? |
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find class detection |
select chimera -> clash detection -> find classes |
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