RBVI 2011 Renewal Ideas and Discussions

Table of Contents

• Table of Contents

Overview

Technology Research and Development Projects

TR&D #1: Chimera Molecular Modeling Environment

• Core 1 Chimera ideas
• Core 1 outline​

TR&D #2: Software for Interactive Analysis of Large Molecular Assemblies

• Core 2 Specific Aims​
• Core 2 early planning, EM and Molecular Assemblies, slides from December 3, 2010 planning meeting.
• Core 2 summary​
• TR&D 2 Final​

TR&D #3: Structure-Function Linkage Database

• Core 3 Specific Aims

TR&D #4: Integrated Analysis and Visualization of Biological Context

• Core 4 Specific Aims
• Core 4 Draft

Driving Biomedical Projects

• DBP #1: Modeling Macromolecular Assemblies - Andrej Sali
• DBP #2: Enzyme Function Initiative - John Gerlt
• DBP #3: Parasitic Disease Pathways - Jim McKerrow
  • DBP3 From Gigi
• DBP #4: HIV Accessory and Regulator Complexes - Nevan Krogan/Yifan Cheng
  • DBP4​, draft of cryoEM part, Yifan has reviewed it.
• DBP #5: 3D Architecture of Hair Cell Stereocilia - Manfred Auer
  • draft​ from Manfred
• DBP #6: Modeling Biological Assemblies from cryoEM Maps - Wah Chiu
  • DBP6 final version​
• DBP #7: Data Validation and Web Visualization at the EMDB and PDB - Berman/Chiu/Lawson/Westbrook/Dutta
  • EM validation task force summary​ from Cathy Lawson
  • DBP7 final version​
• DBP #8: Network Visualization of Genome Assembly Experiments - DeRisi
• DBP Table

Collaboration and Service

1. Integrating Chimera into the NRAMM Automated Processing Pipeline
   • Investigators: Bridget Carragher and Clint Potter, Scripps Research Institute
   • Grant: NIH P41 RR017573
   • Collaboration #1​ from Clint Potter.
2. Molecular animations
   • Investigators: Graham Johnson
3. Protein Polymorphism
   • Investigators: Tom Alber and Paula Therese Lang, University of California, Berkeley
4. Pharmacogenetics of Membrane Transporters
   • Investigators: Kathleen Giacomini and Deanna Kroetz (UCSF)
   • Collaboration #4​
5. Integration of Methods of Structural Analysis of Functional Site: Active Site Profiling
   • Investigator: Jacquelyn Fetrow, Wake Forrest University
   • Grant:
   • Collaboration #5
6. Images and Analysis for the Virus Particle Explorer Database
   • Investigator: Vijay Reddy, Scripps Research Institute
   • Grant: NIH P41 RR012255
   • Collaboration #6​
7. Pipeline for Identifying Pathogen-Host Mechanisms via Systems Biology
   • Investigators: Allan Kuckinsky, Agilent Foundation; Nevan Krogan, UCSF
   • Grant: Agilent (no grant number)
   • Collaboration #7
8. MMTK Integration with UCSF Chimera
   • Investigator: Jean-Didier Maréchal and Victor Munoz, Universitat Autònoma de Barcelona
   • Grant: Spanish Ministry of Science and Innovation, grants CSD2007-00006 and CTQ2008-06866-C02-01
   • Collaboration #8​
9. National Resource for Network Biology
   • Investigators: Trey Ideker, Gary Bader, Alex Pico, and Bruce Conklin
   • Grant: NIH P41 RR031228
   • Collaboration #9
10. Remote User Support and Bug Tracking
    • Investigators:

• Collaboration section (incomplete)
• Collaboration and Service Table

Training

Appendix

• Items for inclusion on Appendix CD-ROM

Documents

• Overview of P41 requirements and deliverables
• 2006 RBVI Grant

Action items (partial list)

• Update these web pages:
  • www.cgl.ucsf.edu/Outreach/Dissemination/index.html