Changes between Version 3 and Version 4 of Grant/chimeraplan

Timestamp:

Mar 18, 2011, 10:08:45 AM (15 years ago)

Author:

meng

Comment:

--

Grant/chimeraplan

@@ -7 +7 @@
   * Integration for systems biology and network visualization
   * Modeling with residue-residue networks
+    * structure in Chimera -> network in Cytoscape, based on residue-residue distance cutoff (as would be used by coarse-grained models), contacts (from Find Clashes/Contacts), or H-bonds
+    * as above except chain-chain instead of residue-residue, edges annotated with numbers of contacts
   * Analysis with pathway networks
  - Interface to ChIMP
@@ -13 +15 @@
   * Help users with dissemination
  - Analysis improvements
-    * structure in Chimera -> network in Cytoscape, based on:
-      * residue-residue distance cutoff (as would be used by coarse-grained models)
-      * residue-residue contact (from Find Clashes/Contacts)
-      * H-bonding (from FindHBond)
-      * as above except chain-chain instead of residue-residue (i.e. diagram of complex), edges annotated with numbers of contacts
     * structure in Chimera -> residue-residue contact map (2D plot)
     * trajectory timeline plots of various measurables
@@ -32 +29 @@
   * (Multiple) Sequence alignment service?
   * Autodock?
+  * coarse-grained dynamics, NMA (unless included with Chimera)
+  * connect to services (not necessarily our own) for protein classification or domain prediction
  - 3D/Stereo output
   * 3D TV