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
  • 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 -> 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
• 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?
• 3D/Stereo output
  • 3D TV
  • YouTube videos
  • Linked to animation?
• New devices (iPad, Android tablets)
  • Support via web (new core?)