research advances
October 2009 news
Spotlight on Structural Genomics
PSI-SGKB [doi:10.1038/nw_psisgkb.2009.47]
PSI:Biology videocast, CASD-NMR, new Propose Targets portal, and more.
NIGMS PSI directors host Q&A videocast about PSI:Biology Network
On 31 August, Jeremy Berg (Director of the NIGMS), Cathy Lewis (PSI Network Director) and Peter Preusch (Acting PSI Director) hosted a lively discussion via videocast about the recently released requests for applications (RFAs) that will establish the PSI:Biology Network. The panel answered questions from a live audience on a wide range of topics, discussing the extended deadlines (October 28), the target selection and proposal process, the new Consortia for High-Throughput-Enabled Structural Biology partnerships (RFA-GM-10-007 or “RFA #3”), and help on construction of the budgetary sections. Questions included: “Do I need to establish partnerships ahead of time in order to apply for RFA #3?” (answer: "No, but if you have one in mind, tell us”); and “Can I propose sequences other than protein sequences?” (answer: "Yes!"). This useful discussion should help many that are assembling their applications now.
Need a cheat sheet? Here are the useful URLs mentioned during the videocast:
Establishing PSI:Biology partnership opportunities: http://www.nigms.nih.gov/Initiatives/PSI/psi_biology/contacts.htm
PSI Sequence Analysis and Comparison Tool (to generate target lists for your grant application): http://cnt.psi-structuralgenomics.org/CNT/targetlogin.jsp, top form.
To propose targets to the PSI-2 Network now, you can use the same site as above: http://cnt.psi-structuralgenomics.org/CNT/targetlogin.jsp, bottom form.
An FAQ about the PSI:Biology RFAs is also available.
Did you miss it? Grab a coffee and watch the 2 hour briefing from the NIH Videocast website. If you have further questions that were not addressed during the briefing, send them to Peter Preusch Email: preuschp@nigms.nih.gov.
PSI part of worldwide NMR software experiment
This month, a correspondence article in Nature Methods highlights the PSI NESG as an active participant in a new worldwide Critical Assessment of Automated Structure Determination by NMR (CASD-NMR) experiment. This experiment will provide pre-release partial NMR datasets so that structural methods groups can assess newly developed methods for automatic NMR data analysis. At least one dataset will be provided by the PSI NESG per month, available from the Get Test Datasets site on the SGKB.
Read the official NIGMS publication article here or find the Nature Methods article doi:10.1038/nmeth0909-625 for more details.
CASD-NMR: critical assessment of automated structure determination by NMR.
A. Rosato et al.
Nat. Methods 6, 625–656 (2009).
[doi:10.1038/nmeth0909-625]
New version of “Propose Targets” now available
Have you tried the new PSI Community-Nominated Targets portal? Accessible from the homepage under “Propose Targets”, we have recently enhanced it by providing users with preliminary reports of similar structures, models and targets in the Protein Data Bank and SGKB, and crystallization propensities calculated by XtalPred (PSI JCSG) and PXS (PSI NESG). You can submit one or many sequences in FASTA format for analysis and then edit them individually and recalculate to improve your scores. These results can give you a hint of how successful your proposed sequence will be experimentally.
You can use this enhanced tool in two ways:
(a) The Sequence Comparison and Analysis tool (SCA-tool) is unrestricted, like XtalPred or BLAST. Insert your sequence(s) in the text box, provide your email address, and a pdf report with the results will be sent to your address upon completion.
(b) PSI-2 Target Nomination should be used to propose protein sequences for structural determination by the PSI-2 Network. Users can create an account to store proposals privately, and submits a proposal with sequence(s) and explanation for review to the PSI-2 Target Selection Committee. The same analysis is conducted as above and is included in the proposal to the committee. Answers are usually received within 1 month.
If you have any questions regarding scientific proposals and issues, please contact Dr. Ward Smith (NIGMS).
Coming to a conference near you
Want to learn more about the PSI Structural Genomics Knowledgebase? Representatives will be available at these upcoming meetings.
American Society for Cell Biology Annual Meeting
5–9 December 2009
San Diego, California, USA
Keystone: Structural Genomics: Expanding the Horizons of Structural Biology
8–13 January 2010
Breckenridge, Colorado, USA
Biophysical Society
20–24 February 2010
San Francisco, California, USA
