Tag Archives: drug targets

Video Tip of the Week: BindingDB for binding affinities

Recently when I was adding videos to our SciVee collection, I noticed that there was a set of new videos about BindingDB. This database has been around for a long time, and I was surprised to realize that we hadn’t covered it yet. And it certainly only grows more important to understand proteins and their binding partners–whether they are other proteins or chemical compounds that can be important effectors of health and disease.

For a decade now this database has been curated and maintained to provide access to information from publications that is often not easily accessible. As their homepage says today:

BindingDB contains 832,773 binding data, for 5,765 protein targets and 362,123 small molecules.

That’s a lot of information available to you to investigate that they have collected. You can start with a protein of interest, or a compound, or a paper, and find related information from those points. There are various other tools and entry points as well.

In addition, it is integrated with many other key resources, including PDB and UniProt, MMDB and KEGG, and more. ChEMBL links offer handy links to compounds.

You can see from their “News” that they are actively maintaining this site, and are developing new tools to offer users ways to interact with the data. But the newest feature seems to be their videos–I’ll let them show you more about how to use their site.

BindingDB: Find and view all data for a target of interest

They offer several other quick tips on ways to interact–starting with an article and obtaining the data, and more. You can access them from the end of the video in the “Related” links, or explore their SciVee set. They are also found on the homepage of BindingDB right now. So check them out if you need protein binding data. They may have what you seek.

 

Quick link:

BindingDB site: http://bindingdb.org/

Reference:

Liu, T., Lin, Y., Wen, X., Jorissen, R.N. & Gilson, M.K. (2007). BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities, Nucleic Acids Research, 35 (Database), D198. DOI: 10.1093/nar/gkl999

Tip of the Week: TDR Targets Database

tdr_targets_tip  For today’s tip, I would like to introduce you to the TDR Targets Database, which seeks “… to exploit the availability of diverse datasets to facilitate the identification and prioritization of drug targets in pathogens causing neglected diseases.” I found out about this database this past weekend as I was catching up on my ‘science reading’. The database was featured in an article published November of 2008 in Nature Reviews Drug Discover – if you have a subscription, I’ve cited it below. Even though the article is a bit old, it seems very timely for us here at OpenHelix right now since in February Trey participated in the first annual African Virtual Conference on Bioinformatics 2009, and later this week he is heading off to give a talk at the Genetics and Genomics of Infectious Diseases conference in Singapore. TDR Targets is a nice resource – here I show a few search options, but there is so much more here that you can explore on your own!

ResearchBlogging.org Agüero, F., Al-Lazikani, B., Aslett, M., Berriman, M., Buckner, F., Campbell, R., Carmona, S., Carruthers, I., Chan, A., Chen, F., Crowther, G., Doyle, M., Hertz-Fowler, C., Hopkins, A., McAllister, G., Nwaka, S., Overington, J., Pain, A., Paolini, G., Pieper, U., Ralph, S., Riechers, A., Roos, D., Sali, A., Shanmugam, D., Suzuki, T., Van Voorhis, W., & Verlinde, C. (2008). Genomic-scale prioritization of drug targets: the TDR Targets database Nature Reviews Drug Discovery, 7 (11), 900-907 DOI: 10.1038/nrd2684