= 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 || ||
|| 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 Subgene''''''Viewer plugin ||


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