Changes between Version 9 and Version 10 of HIVspikes

Timestamp:

Sep 25, 2009, 4:27:03 PM (17 years ago)

Author:

goddard

Comment:

--

HIVspikes

@@ -70 +70 @@
 [[Image(gp120_15models_mav.png)]]
 
+Should show more v3 loop sequences in MAV to see conserved regions.
+Compare those to contacts in a structure having V3 loop.
+
+
 Loading the top 13 blast hits shows they are all quite similar structures:
 
@@ -114 +118 @@
 to see the dense coverage by sugars.
 
+== Cytoscape ==
+
+Would like to demonstrate network visualization of HIV sequence strains clustered
+into clades.  Associate gp120 structures with sequences and be able to see what
+clades the structures belong too.  (All clade B, US/Europe?)
+
+[[Image(hiv_clades.gif)]]
+
+Thousands of HIV complete rna sequences available.  Not sure how to measure similarity
+for cytoscape clustering.  Also technical problem to associate PDB gp120 structures with
+those sequences.
+
 {{{
-
 
 SAXS profile of gp120 / FAB / CD4 complex.
 
 Make plastic model of gp120 trimers in 5 parts with bound CD4 and FAB
-connected by magnets.
-
-Cytoscape showing clustered HIV sequences clustered into clades
-with associated PDB structures.
-
-Should show more v3 loop sequences in MAV to see conserved regions.
-
-
-Only one gp120 (SIV) has glycans.  Might demonstrating adding
-them to naked gp120?
+connected by magnets, pieces colored distinctly.
 
 }}}