Not enough hits.

Not enough hits.

Postby SambaY » Sun Apr 03, 2011 2:34 pm

Hi, I'm trying to pick the residues with the lowest change in G(FC) and a higher change in SASA% and after submitting my query under "pharmacohpore" I keep getting only 0 hits or 13 hits both before and after I make some changes. Am I starting with the wrong types of residues or is 13 hits okay (I thought we wanted to started with thousands of hits).

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Re: Not enough hits.

Postby dkoes » Fri Apr 08, 2011 8:54 am

The number of hits will depend on the pharmacophore. You will need to edit the default one generated from the residues you selected. For example, you can increase the tolerance off the hydrogen bond features, removing some features optional, remove directionality constraints, or increase the pivot value of the anchor. I bet if you remove (or make optional) a pharmacophore feature from your 13 hit search you will get many more hits.

One of the goals of the assignment is for you to get experience designing pharmacophores through an iterative process where you see what features contribute the most to binding. I would make sure any hydrophobic pockets are filled and then try to satisfy as many hydrogen bonds as possible. Also, sorting/filtering by the number of rotatable bonds will also help you get a good autodock score.
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