Wednesday, February 17, 2010

While we predict drug targets, pharma already knows them

All the excitement about predicting drug targets from remote chemical structure similarities (Nature) and drug side effects (Science) suddenly seems strangely unfounded when you realize that "they" already have the answer:
This figure is a tiny section of the data used for Preclinical Safety Profiling at the Novartis Institutes for BioMedical Research. They are not alone: BioPrint from Cerep is a repository of 2500 compounds assayed against 159 targets. Paolini et al. mention 600,000 binding data points at Pfizer.

Things are begining to change, thanks to academic curation efforts like BindingDB, PDSP Ki database, DrugBank etc. and not least to EMBL-EBI's acquisition of ChEMBL. Still, one can only imaging how different current academic research questions would be if the all-against-all drug–target assay information would be public. In essence, academia is working on predicting additional data points from a sparse matrix, while pharma companies already have the full matrix in hand, but want to add more rows/columns to the matrix in silico.

Update: As always, good discussion on FriendFeed.

Thursday, February 4, 2010

Human Protein Atlas data for download

As I just learned in our lab's journal club, the data from the Human Protein Atlas is available for download, thanks to their recent paper in MSB. Curiosly enough, the HPA help page still states that they do not make data available as a matter of "general policy."