Binding DB from chemistry notes

As brought to my attention by my PI--the Gilson lab at the University of Maryland Biotechnology Institute has been working to develop a database of known protein-ligand binding affinities, also known as the BindingDB. While the BindingDB currently contains only about 15,000 small molecule ligands and 30,000 affinities to proteins measured through isothermal titration calorimetry (ITC) and enzyme inhibition methods, the database is rapidly increasing in size, at a rate of about 10,000 new data points per year.

You can search for your favorite protein or ligand, but there are also several other search features such as molecular weight, K_i, and substructure. Users are encouraged to deposit data from their own published binding experiments, so hopefully this database will continue to grow in the future. Once enough information has been collected, I can imagine that the BindingDB will become a powerful tool in drug discovery--Not only can you download computer models of compounds and affinity measurements, but there is also an interesting virtual screening section of the website that I'd like to explore when I have some spare time.

Of course, this isn't the only database that characterizes molecular interactions. Some of the others include:

• Database of Interacting Proteins (DIP)
• Protein-Nucleic Acid Interactions (ProNit)
• K_iBank
• PDBBind Database