David Koes edited ER_b_ER_b_with__.tex  over 8 years ago

Commit id: d1ad3af925e391e1d12d4cf45efca1e376863dc0

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ER-b \subsection*{ER$\beta$}  ER-b with its best SMARTS expression and approach performed better than random performance for both FOMS and VAMS (cite stats table). VAMS performed slightly better than FOMS for ER-b, and the difference was significant (cite stats table). This indicates that VAMS is the best pre-screening method for ER-b.  As might be expected, the binding pocket of ER-b is very similar to ER-a, as is the mode of its inhibition. Similar to ER-a inhibitors, a hydrogen bond donor/acceptor interaction is necessary for interacting with Glu305 and Arg346. In addition, there is another hydrogen-bond donor interaction with His475 (cite ER-b). This indicates that both of these interactions are key to the binding mode of ER-b inhibitors. Only the Glu305 and Arg346 interactions are covered by our SMARTS expressions and fragment pre-alignments. This means that the other key interaction involving the conserved His on the distal side of the steroid would not be covered. This means that the FOMS approach could accept a compound with only the Glu and Arg interactions, while this type of compound would not actually bind (i. e. pick up a decoy). There are other important hydrophobic interactions evident from the binding of the inhibitor to ER-b, however the interactions mentioned above seem the most important (cite ER-b).