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PSI in the Spotlight

July 2012

SBKB [doi:10.1038/sbkb.2011.90]

TargetTrack Database Accepts 300,000th Structure Determination Target

More than 300,000 protein sequences selected for structure determination have now been deposited to TargetTrack, the open structural proteomics experimental data tracking resource. Nearly 200 targets are added and thousands of histories are updated on a weekly basis by our contributors.

TargetTrack is the latest version of the Protein Structure Initiative's target registration database, having replaced TargetDB (created by the RCSB PDB in 2003) and PepcDB (created in 2006) in April 2012. Its MySQL database contains contact information, annotations, protocols, trial histories, and current statuses for all registered protein sequences. Contributions include projects from the PSI-1 (pilot), PSI-2 (production), and the current PSI:Biology project, the NIAID-funded Structural Genomics Centers, the UK-Canada Structural Genomics Consortium, several European projects (SPINE, XMTB), and the South African Structural Targets Annotation Database.

TargetTrack encourages other groups to submit their experimental data to provide a resource for experimental data mining. For more information on depositing your group's work, please contact Email: target-help@sbkb.org.

NIH Roadmap Meeting on Membrane Protein Technologies in November 2012

The 4th NIH Roadmap Meeting for Membrane Protein Structures and Complexes will be held at the San Francisco Westin Hotel in downtown San Francisco from Wednesday, November 28, 2012 at 8AM through Friday, November 30, at 12PM. This meeting will be hosted by the Membrane Protein Expression Center (MPEC), one of the membrane protein technology centers funded by the NIH Common Fund Structural Biology Program. The meeting is coordinated by Robert Stroud, director of the MPEC center at UCSF and the PSI Center for Structures of Membrane Proteins (CSMP).

Presentations and discussions will focus on progress as well as overcoming barriers to transform functional expression of membrane proteins and complexes and structure determination at atomic resolution. Corporate participation is encouraged for those companies who are actively developing membrane protein targets or producing equipment and reagents for membrane protein research. Corporate presentations or displays for the meeting are available. For questions about corporate registration please contact Email: mmrmi2012@msg.ucsf.edu.

Save the Date — PSI:Biology Enabling Technologies Workshop Is Back for 2012

Back by popular demand, the PSI:Biology Program will hold the next installment of the “Enabling Technologies” Workshop, presenting the latest technologies and ideas to surpass experimental bottlenecks to protein production and structure determination. This one-day workshop will be held on December 12, 2012 in the Building 49 Auditorium at the NIH campus, Bethesda, MD, USA.

Check back with the SBKB for the latest information on program details, website, abstract submission, and registration.

Updates to the SBKB

This month, we release a new left menu which highlights our new scientific Hubs. These Hubs are designed to collect PSI and SBKB information so that our audience can find features based on their needs.

We've also updated our PSI Community-Nomination Portal (http://sbkb.org/cnt/) to show you the latest structures solved from collaborations within the greater community. You can also view the entire list of structures by clicking “See all” on the CNT homepage. Information about the target and structure can be accessed via the table and gallery.

Current data totals as of 19 June 2012:

 

  • 19 M rows of annotations in SBKB database about 82347 PDB structures and 303,208 structure determination targets in TargetTrack .
  • 22.9 M comparative protein models for 3.8 million UniProt sequences in Protein Model Portal .
  • 1015 experimental protocols referenced in TargetTrack.
  • 300 technology reports in the Tech Portal .
  • 1,752 PSI publications in the Pubs Portal, with 1201 of them having >5 citations.

 

Coming to a Conference Near You

The PSI SBKB regularly attends national and international scientific conferences to talk about the PSI and the SBKB portal with the greater biological community. Meet PSI, SBKB, and PSI:Biology-Materials Repository representatives at our posters, booths, and oral presentations at these upcoming conferences:

2012 Meeting of the American Crystallographic Association
July 28, 2012 – August 1, 2012
Oral presentation at PSI “More Tools for the Home Lab” Session on Sunday, July 29
Boston, MA, USA

26th Annual Symposium of the Protein Society
August 5, 2012 – August 8, 2012
San Diego, CA, USA

Margaret Gabanyi

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