Ideas and discussions for the RBVI 2011 Site Visit

Scenarios

Scenario 1

• SFLD/Cytoscape/Chimera
• (Scenario #1 from 2009 Advisory Committee mtg: ​https://plato.cgl.ucsf.edu/trac/SFLD/wiki/RBVIAdvisoryCommitteeMeeting#no1)

Scenario 2

• Chimera/Volume Tools/Cytoscape(?)
• (Scenario #2 from 2009 Advisory Committee mtg: ​https://plato.cgl.ucsf.edu/trac/chimera/wiki/HIVspikes)

Ideas of what to show

TR&D 1

TR&D 2

• Building a "composite model" and linking molecules, maps and sequences of components.
• Chimera analysis web log. Would be cool to demo WebGL embedded in Chimera log then shown on a smart phone or tablet as a way to facilitate hallway/lecture-hall/lunch collaborative work.

Biological Systems

• ​HIV Capsid - Illustrates composite model building of HIV conical core particle. Capsid protein interfaces highly conserved drug target (June 2011 PNAS ​paper)
• ​HIV RNA - Secondary structure of full HIV RNA, I made 3-d model and animation with Chimera script. Nature 2009 ​paper).
• ​Dengue virus - Maturation of dengue virus involves major rearchitecting of capsid. Chimera animation shows hypothetical model from Michael Rossmann lab.
• ​Termite gut - Segmentation tool demo.
• ​Muscle filaments, myosin / actin / tropomyosin. Another good "composite" model example. Haven't done much with this system yet though. Recent Roger Craig / Raul Padron ​paper, PNAS July 2011

TR&D 3

TR&D 4

• Incremental loading of networks
• Fuzzy clusters
• Invoking Cytoscape from Chimera
• SFLDLoader2??