Hey everyone! We will be having an Office Hour led by rmoretti at 12 PM central time (5 PM GMT) on Saturday, July 2nd. Feel free to bring all questions but, if you have small molecule design questions, definitely bring those this time around!

(Wed, 06/29/2022 - 20:31  |  3 comments)
spvincent's picture
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I'm wondering how many

I'm wondering how many submitted solutions contain atoms other than CON. The interface allows you to add things like CF3 groups but despite the fact that these seem to occur regularly in drug molecules there always seems a penalty when you try to use them in Foldit.

(I'm out for office hour)

rmoretti's picture
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See Discord

Discord should have a copy of the office hour, and Susume helpfully repeated your question there.

I've copied highlights below:

Regarding atom types, there's no specific penalty for non CON atoms (aside from the atom count objective on the recent KLHDC2 puzzle series.) That said, the other atom types are only going to make sense if they fit energetically with the rest of the protein. I haven't looked at the rate of non CON atoms in the results -- I think there are some, but possibly not many.

But it's also true that adding other atoms is sometimes a late stage optimization in "normal" drug design -- early stage compounds do tend to be CON heavy, even in non-Foldit contexts.

I think that P,S, Cl and F should be usable in the right circumstances. You are correct that the current scoring hasn't really been optimized for those sorts of non-protein atoms (the most work on the score function is for protein interactions). We may need to come back and tweak how those atom interactions are scored for better results.

agcohn821's picture
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Office hour

Hi everyone--a transcript of the latest office hour has been posted in the forum!


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