Tag Archives: drug discovery

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

Guest Post: New features at CTD – Allan Peter Davis

This next post in our continuing semi-regular Guest Post series is from Allen Peter Davis, of Comparative Toxicogenomics Database (CTD) at Mount Desert Island Biological Laboratory (MDIBL). If you are a provider of a free, publicly available genomics tool, database or resource and would like to convey something to users on our guest post feature, please feel free to contact us at wlathe AT openhelix DOT com.

The Comparative Toxicogenomics Database (CTD) is a free, public resource that promotes understanding about the effects of environmental chemicals on human health.  Since Trey’s original Tip of the Week about CTD, we’ve added many new features we’d like to highlight.

* The redesigned CTD homepage makes navigation easier and more intuitive.  Check out the keyword quick search box on every page, and try the “All” setting to see the scope of information available at CTD.

* A new Data Status page uses tag clouds to display the updated content for that month.

* We are particularly pleased to announce new statistical analyses of CTD data.  Chemical pages now feature enriched Gene Ontology (GO) terms, garnered from the genes that interact with a chemical.  In this release, CTD connects over 5,000 enriched GO terms to more than 4,500 chemicals.  As well, now our inferred chemical-disease relationships are also statistically scored and ranked.  Both new features will help users explore and generate testable hypotheses about the biological effects of chemicals.

* GeneComps and ChemComps discover genes or chemicals with a similar toxicogenomic profile to your molecule of interest.  Learn more about this feature in our recent publication.

* Reactome data are now also included with KEGG, for a more comprehensive view of pathways affected by chemicals.

VennViewer and MyGeneVenn are new tools that compare datasets for chemicals, diseases, or genes (including your own gene list) using Venn diagrams to discover shared and unique information.  These two visualization tools are a nice accompaniment to our original Batch Query tool for meta-analysis.

* The FAQ section under the “Help” menu provides examples of how to maximize your experience with CTD.

* Download our Resource Guide (pdf link) to keep as a handy reference card for CTD.

From the homepage, you can also subscribe to our monthly email newsletter to keep current with CTD’s growing content and features.  You can always contact us to request curation of your favorite chemical or paper.  And with our new “Author Alert” email program, we’ll even contact you to let you know when we’ve curated data from one of your publications in CTD.

We strive to be the best possible resource of chemical-gene-disease networks for the biological community, so feedback and input from users are of great importance to us.

- Allan Peter Davis

A shout out or two, Bork paper and on the shoulders of giants…

Just thought I’d give a shout out… two in fact:

First, my former Postdoc advisor, Peer Bork, and lab just published an excellent paper in Science entitled “Drug Target Indentification Using Side-Effect Similarity.” It’s an excellent example of the marriage of computational genomics and experimental biology. Fascinating stuff (I’m only slightly biased, but it is). I’ll do a more in depth review later.

Second, Bora at Blog Around the Clock got together with gg of skullsinthestars and created a “The Giant’s Shouldersblog carnival. This grew out of the Classics Challenge  ( “read and research an old, classic scientific paper and write a blog post about it”) at skullinthestarts (which our own Mary had an excellent submission to if I do say so myself). It was so popular they decided to make it a monthly thing. Which is good, because now I can do the one I wanted to do before for August’s carnival. July’s carnival is here at Blog around the Clock.