Tag Archives: homology

Video Tip of the Week: The PSI SBKB’s New Content Hubs


In today’s tip I will feature the newly organized content hubs over at the Protein Structure Initiative’s Structural Biology Knowledgebase, or PSI SBKB. We do have a free, full-length tutorial on the PSI SBKB that we are in the process of updating, but I thought I’d just touch on one of the new updates to the PSI SBKB now while it is “hot”. :) Quoting from their PSI: Biology in the Spotlight, July 2012 News:

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.

I’ve been working with these hubs over the last several months, and have gotten to watch as they have been developed. These scientific hubs make it easy for users to access specific content offered by both the SBKB and the PSI as a whole, because they are organized by content. I think the new left-hand organization is nice – the bright banner and organization will highlight these hubs to users, who will hopefully take full advantage of the resources found in each hub. Currently the scientific hubs are organized around the following content: targets; protein structures, sequences and function; membrane proteins; homology models; and methods. In the tip video I briefly visit the membrane proteins hub and the methods hub to give you an idea of the types of links and contents that you will find, but so be sure to check them out on your own to see what resources you can find for furthering your research.

For further details on the PSI SBKB, see the links below & stay tuned for our full, updated tutorial coming free to a browser near you! :)

Note: the open access papers will not cover the new hubs, but will describe many of the resources accessible from the hubs.

Quick links:
PSI Structural Biology Knowledgebase resource: http://www.sbkb.org

OpenHelix Introductory tutorial on the PSI SBKB (free to access):
http://www.openhelix.com/sbkb

Related resource – RCSB Protein Data Bank (RCSB PDB): http://www.rcsb.org

Related OpenHelix Introductory tutorial on the RCSB PDB (free to access):
http://www.openhelix.com/pdb

PSI SBKB References:

Gifford LK, Carter LG, Gabanyi MJ, Berman HM, & Adams PD (2012). The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource. Journal of structural and functional genomics, 13 (2), 57-62 PMID: 22527514  (requires subscription)

Gabanyi MJ, Adams PD, Arnold K, Bordoli L, Carter LG, Flippen-Andersen J, Gifford L, Haas J, Kouranov A, McLaughlin WA, Micallef DI, Minor W, Shah R, Schwede T, Tao YP, Westbrook JD, Zimmerman M, & Berman HM (2011). The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. Journal of structural and functional genomics, 12 (2), 45-54 PMID: 21472436 (open access here)

Cormier CY, Park JG, Fiacco M, Steel J, Hunter P, Kramer J, Singla R, & LaBaer J (2011). PSI:Biology-materials repository: a biologist’s resource for protein expression plasmids. Journal of structural and functional genomics, 12 (2), 55-62 PMID: 21360289 (open access here)