The increase of compound phenotypic screenings over the last years has dramatically increased the number of small molecules with non-annotated protein targets [40—42].

Other methods use local structural comparisons of small molecule binding sites to infer the localization and specificity of binding pockets [25,26] as well as to infer new ligand interactions in known binding pockets [27].

Here, we describe the method alongside the predictions for all the small molecule drugs present in DrugBank [32] against the human 3D proteome.

Briefly, the RFC classifier predicts whether two small molecules are likely to bind the same target-binding site by comparing their structural and chemical properties.

Since structurally similar binding sites are more likely to bind the same small molecule .

Although small changes in the catalytic site could have a dramatic impact on the bind-ing-affinity of a small molecule , the overall high similarity among the Sorafenib predicted binding sites shows a clear trend towards binding site conservation within this set of proteins.

concentrations of the GR agonist Dex including EtOH in the presence of different concentrations of APILUC reporter plus one of three added cofactors: the plasmid for TIF2 or two small molecules (NU6027 and phenanthroline) recently identified in a high throughput screen as accelerators of GR transactivation [30].

4 and 5 show that the dose-response parameters are also well fit by linear-fractional functions for the small molecules NU6027 and phenanthroline [30].

Using the extensively characterized system of GR repression of APl induction in UZOS.rGR cells with a transiently transfected synthetic reporter [8,15,28,29] , we show that four factors (the reporter gene, TIF2, and two small molecules [30]) have the same kinetically-defined mechanism and position of action as in GR-regulated gene induction.