RBVI 2011 Renewal Ideas and Discussions

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​
  • Core 2 draft

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
• DPB #2: Enzyme Function Initiative - John Gerlt
• DPB #3: Parasitic Disease Pathways - Jim McKerrow
• DPB #4: HIV Accessory and Regulator Complexes - Nevan Krogan/Yifan Cheng
• DPB #5: Physical Science in Oncology - Manfred Auer
• DPB #6: Visualization of Biological Assemblies at Intermediate Resolution - Wah Chiu
• DPB #7: Data Management at the RCSB-PDB - Berman/Lawson/Westbrook
• DPB 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

1 Molecular animations

• Investigators: Graham Johnson

1 Protein Polymorphism

• Investigators: Tom Alber and Paula Therese Lang, University of California, Berkeley

1 Pharmacogenetics of Membrane Transporters

• Investigators: Kathleen Giacomini and Deanna Kroetz (UCSF)

1 Integration of Methods of Structural Analysis of Functional Site: Active Site Profiling

• Investigator: Jacquelyn Fetrow, Wake Forrest University
• Grant:

1 Chimera Images for the ViperDB Database

• Investigator: Vijay Reddy, Scripps Research Institute
• Grant:

1 Shared postdoc – Project Title?

• Investigators: Allan Kuckinsky, Agilent Foundation; Nevan Krogan, UCSF
• Grant: Agilent (no grant number)

1 MMTK Integration with UCSF Chimera

• Investigator: Jean-Didier Maréchal and Victor Munoz, Universitat Autònoma de Barcelona
• Grant:

1 National Resource for Network Biology

• Investigators: Trey Ideker, Gary Bader, and Bruce Conklin
• Grant:

1 Remote User Support and Bug Tracking

• Investigators: [

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