== Chimera Grant Ideas ==

 - Refactor
  * Qt, gtk for desktop
  * WebGL, jQuery for web (new core?)
 - Interface to Cytoscape
  * 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
  * Integration for larger scale structures (w/ Assemblies core)
 - Animation
  * Help users with dissemination
 - Analysis improvements
    * structure in Chimera -> residue-residue contact map (2D plot)
    * trajectory timeline plots of various measurables
 * Sequence information
   * Compact depiction of large alignments as histograms (ala Profile Grids)
   * Improved ability to map sequence markups to structure
    * BLAST to identify
    * align input to BLAST result
   * Gather info from additional databases (currently only !UniProt)
  * Include more computation tools (minimization, MD, NMA, etc)
  * Take advantage of desktop computing power and web services
 - Web services
  * ChIMP tools
  * (Multiple) Sequence alignment service?
  * Autodock?
  * coarse-grained dynamics, NMA (if not 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
  * !YouTube videos
  * Linked to animation?
 - 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)