research advances
February 2012 news
PSI:Biology in the Spotlight
SBKB [doi:10.1038/sbkb.2011.65]
CAMEO to test modeling methods, 2012 calendars, NIH Roadmap meeting, and more...
2012 Calendars Are Here!
Due to the popularity of our 2010 calendar, the PSI SBKB has created a 2012 calendar, illustrated with stories from our Featured PSI Molecules and Systems highlights. If you would like one (or several), send your name, affiliation, and mailing address to the PSI SBKB team at Email: comments@sbkb.org.
Can't wait several days for the calendars to arrive? Download the pdf version right now.
New CAMEO Modeling Server to Assess Methods
Different computational tools have different strengths and weaknesses. The retrospective evaluation of the accuracy of predictive methods is crucial from both a user and a methods developer perspective in order to establish the state of the art, and to select the most appropriate methods for a specific task.
The goal of the CAMEO (Continuous Automated Model EvaluatiOn) project is to continuously evaluate the accuracy and reliability of protein structure prediction services in a fully automated manner. The retrospective evaluation of prediction accuracy helps users select the most suitable tool for a given modelling problem. CAMEO makes use of pre-released sequences of new PDB entries, which are sent to participating servers. The results are returned and collected before the coordinates are publicly released by the PDB.
CAMEO (http://www.cameo3d.org) is a community project initiated by the “Working Group on Theoretical Structural Models Validation” as part of the Protein Model Portal of the PSI SBKB. We invite developers of prediction methods to participate by registering their servers to CAMEO. In the current release, CAMEO addresses the evaluation of services for protein structure prediction. In the coming months, we plan to open CAMEO for assessment of “Ligand Binding Site Predictions” and “Model Quality Estimation Tools.”
The CAMEO project will be briefly presented at the upcoming Keystone meeting on High-Throughput Structural Biology (January 22 - 27, 2012, Keystone, Colorado). We would be happy to discuss CAMEO with you during the meeting, or to receive your feedback and comments via email at Email: help-cameo@proteinmodelportal.org.
Meeting on Membrane Protein Technologies Coming 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, 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, UCSF and the PSI Center for Structures of Membrane Proteins (CSMP).
All members of the membrane protein structure community are invited to participate in this expanded meeting by submitting abstracts for presentations and posters. This series of meetings has been very successful in generating open exchange and sharing of technologies, materials, and ideas focused on targeting membrane protein structure determination. This fourth meeting in the series provides a unique opportunity for investigators engaged in developing and applying new technologies for structural biology of membrane proteins and complexes to focus on technologies that facilitate membrane protein structure determination and recent structures of membrane proteins.
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: mrmi2012@msg.ucsf.edu.
TargetDB and PepcDB Resources Retiring Soon
Update your web browser bookmarks!
On or about February 1, 2012, the existing TargetDB and PepcDB experimental data tracking databases will be replaced with a new single resource, TargetTrack (http://sbkb.org/tt/). If your site depends on either these two services, please email Email: target-help@sbkb.org for assistance with this transition.
Updates to the SBKB
Current data totals as of 6 January 2012:
- 19 M rows of annotations in SBKB database about 77546 PDB structures and 286,864 SG structure determination targets in TargetTrack.
- 22.3 M comparative protein models for 3.8 million UniProt sequences in Protein Model Portal
- 905 experimental protocols referenced in TargetTrack.
- 254 technology reports in the Tech Portal
- 1,678 PSI publications in the Pubs Portal, with 1152 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 and booths at these upcoming conferences:
Keystone: Structural Biology of Cellular Processes, running co-jointly with
Keystone: High-throughput Structural Biology
22 January 2012 – 27 January 2011
Keystone, Colorado, USA
Biophysical Society
25 February 2012 – 29 February 2012
San Diego, California, USA
