Tag Archives: model

Tip of the Week: From UniProt to the PSI SBKB and Back Again


It is often beneficial to visit multiple biomedical databases or resources, even if they seem to provide overlapping¬† information because no two resources focus on the exact same information, or present it in exactly the same way. Instead of duplicating each others’ curation efforts, database often link out to related information at other resources. You can think of these links as “social connections”, if you want and in today’s tip I want to show you a couple of connections between protein information resources, including a new connection that really features some of the core value of the PSI’s Structural Biology Knowledgebase, or SBKB.

I begin the tip at the UniProtKB, where I search for a UniProt ID number. From the resulting protein report I first briefly show you how to link out to a corresponding RCSB PDB report, where you can find high quality protein structure information and more. If you are interested in learning more about the RCSB PDB & how to use it, please check out OpenHelix’s full, free tutorial that is sponsored by the RCSB PDB.

From there I return to the UniProt report and demonstrate a new link out option that links to protein protocols, available materials, as well as information about theoretical models and predicted protein targets from the SBKB. I don’t have time to show it but a recent update to the SBKB allows users to now search the Structure Biology Knowledgebase with a UniProt accession number. These searches provide users with additional information including protein structure information and information about pre-released structure sequence. As with the RCSB PDB, we have a free tutorial on the SBKB that is sponsored by the Protein Structure Initiative.

As I scroll through the UniProt protein report users will see information and links for a wide variety of bioscience resources. OpenHelix, as I’m sure many of you are aware, has tutorials on how to use many of these resources. Our tutorials on the RCSB PDB and the PSI SBKB are both free. Our tutorials on UniProt and many other resources are available through a subscription to our database of trainings or through purchase of individual access. Whether you learn the resources through our tutorials, through the references I list below, or through your own explorations of the databases, there really is an amazing amount of information available through these interlinked, publicly-funded resources – please make use of them in your research!

Quick Links:

UniProt Knowledgebase -  http://www.uniprot.org/

OpenHelix Tutorial on UniProt – http://www.openhelix.com/cgi/tutorialInfo.cgi?id=77

RCSB PDB – http://www.pdb.org

OpenHelix Tutorial on the RCSB PDB – http://www.openhelix.com/pdb

The Protein Structure Initiative Structural Biology Knowledgebase (SBKB) -  http://www.sbkb.org/

OpenHelix Tutorial on the SBKB – http://www.openhelix.com/sbkb

Catalog of all OpenHelix tutorials – http://www.openhelix.com/cgi/tutorials.cgi

References:
The UniProt Consortium. (2009). The Universal Protein Resource (UniProt) in 2010 Nucleic Acids Research, 38 (Database) DOI: 10.1093/nar/gkp846

Rose, P., Beran, B., Bi, C., Bluhm, W., Dimitropoulos, D., Goodsell, D., Prlic, A., Quesada, M., Quinn, G., Westbrook, J., Young, J., Yukich, B., Zardecki, C., Berman, H., & Bourne, P. (2010). The RCSB Protein Data Bank: redesigned web site and web services Nucleic Acids Research, 39 (Database) DOI: 10.1093/nar/gkq1021

Berman, H., Westbrook, J., Gabanyi, M., Tao, W., Shah, R., Kouranov, A., Schwede, T., Arnold, K., Kiefer, F., Bordoli, L., Kopp, J., Podvinec, M., Adams, P., Carter, L., Minor, W., Nair, R., & Baer, J. (2009). The protein structure initiative structural genomics knowledgebase Nucleic Acids Research, 37 (Database) DOI: 10.1093/nar/gkn790