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)