Changes between Version 4 and Version 5 of Grant/chimeraplan

Timestamp:

Mar 18, 2011, 10:35:35 AM (15 years ago)

Author:

meng

Comment:

--

Grant/chimeraplan

@@ -30 +30 @@
   * Autodock?
   * coarse-grained dynamics, NMA (unless included with Chimera)
+  * GASPdb search (structure in Chimera as query)
+  * all-by-all BLAST or other similarity network creation protocols (feasible??)
   * connect to services (not necessarily our own) for protein classification or domain prediction
+  * searches against HMM or sequence pattern databases (e.g. SFLD, Superfamily, PFAM, etc.)
  - 3D/Stereo output
   * 3D TV
@@ -37 +40 @@
  - New devices (iPad, Android tablets)
   * Support via web (new core?)
+
+ - Additional sequence-structure-network integration ideas 
+  * structure in in Chimera -> search against SFLD HMMs, return sequence alignments, networks, etc. all annotated with functional residues
+  * multiple sequence alignment in Chimera -> web service network creation
+  * single structure or sequence in Chimera -> web service BLAST, filtering, then network creation
+  * Match->Align for a set of superimposed structures in Chimera now gives similarity values, could also give network (caveat: only feasible on small set of structures)
+  * Chimera extension to view GASPSdb hits (similar to Kavraki Lab's Viewmatch for viewing Labelhash hits, in turn based on Viewdock)