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June 2009

PSI-SGKB [doi:10.1038/nw_psisgkb.2009.27]

PSI SGKB to release beta version

Starting June 1st, a pre-release (beta) version of the PSI SGKB will be available for public testing. Details are provided at the KB Release History page. We invite you to try it out and give us your feedback.

New features include:

  • An expanded protein search capability with the addition of data from over 150 biological and biochemical databases;
  • Integrated visualization of the three-dimensional protein structure and its features using FirstGlance;
  • A tabular summarization of availability of information from the most popular external sequence-, structure- and function-related resources;
  • All related protein properties (annotations) neatly displayed as a notebook and organized by biological category such as 'Gene-level', 'Protein-level', 'Functions' and more;
  • An enhanced community-nominated targets proposal portal which will inform you of similar structures, targets and models, and also predict your sequence's crystallizability as you prepare your proposal; and
  • A new FAQ about how to use the KB's various Web Services to search the database.

As this is a beta version, this new system may still contain bugs that are actively being addressed. To report a bug, email us at Email:; please include the nature of the error and the actions that elicited it.

Data sets for structural bioinformaticians available from the PSI and the SGKB

Did you know that the PSI SGKB provides access to several data sets for methods development? The PSI can provide two collections of data that structural bioinformaticians can use for assessing the accuracy of new methods.

The first is a list of all structures solved by PSI efforts but whose functions have not yet been experimentally determined. The Functional Sleuth, available from the PSI SGKB homepage, challenges the biological community to explore galleries of structures and provide further insights about these macromolecules. They can also serve as test cases for those developing methods for protein function prediction. To learn more about how to obtain this data set, go to our new Web Services page.

In addition, as noted previously, the PSI centers will be permitted to hold a limited number of structures to be used as 'blind test cases' for evaluating new structure-determination methods before the structure is released to the public. In addition, certain data (for example, NMR chemical-shift data or limited numbers of experimental constraints) for these structures will be made available on the public websites of the corresponding PSI centers. Information about available data, along with links to the respective center, are centrally located on the PSI SGKB's See Latest Structures, which is updated weekly.

You can read the full PSI Policy on Structures for Methods Development for more details.

Upcoming Meetings
Want to learn more about the PSI SGKB? Representatives will be available at these upcoming meetings.

39th Mid-Atlantic Macromolecular Crystallography Meeting
28-30 May 2009
College Park (Maryland), USA

17th Annual International Conference on Intelligent Systems for Molecular Biology (ICMB) and 8th European Conference on Computational Biology (ECCB)
27 June-2 July 2009
Stockholm, Sweden

Protein Model Portal
VIII European Symposium of the Protein Society
14-18 June 2009
Zurich, Switzerland

Margaret Gabanyi

Protein Structure Initiative Corner


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