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1432: HIV Protease Inhibitor Small Molecule Design

Closed since over 8 years ago

Intermediate Small Molecule Design Pilot

Summary

Created
September 19, 2017
Expires
Max points
100
Description

This is the first official small molecule design puzzle. The goal is to change the ligand in the center of the protein to find better inhibitors of HIV protease. Use the Ligand Design tool in the selection interface (or the "Ligand Design" mode in the original interface) to alter the chemical identity of the inhibitor. See the blog post for more information on the puzzle and small molecule design.

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Comments

rmoretti Staff Lv 1

We're calling this category of puzzle (one where you modify the chemical identity of a non-protein ligand) "Small Molecule Design".

"Drug design" also works. But "small molecule design" is a little more general, as the molecules we're designing aren't necessarily drugs per se. (Also, protein-based and RNA-based drugs do exist.)

LociOiling Lv 1

It looks like the design queue tool has an interface similar to a manual remix, but the bar underneath the navigation arrows doesn't show "design x of y". (Or anything, actually). This makes it impossible to know how many designs are in the queue.

SaraL Lv 1

Not familiar with the editing process, so I went and changed chemical bonds and swapped out individual atoms, while using the "similarity to known binders" score as a guide. I got up to 40% and couldn't get it any higher.

I attempted to upload my solution to share with my group, but I got a messages saying "Error in sequence."

Back to the drawing board?

Bruno Kestemont Lv 1

I got the same error for some solutions (unable to load or share a saved solution), also with high bonus (>50% similarity) and same method.

See Feedback here:
http://fold.it/portal/node/2004221

Moreover, the related client crashes after some time.

For another solution (with lower bonus), there was no problem.

rmoretti Staff Lv 1

There's going to be a limit to how high the "similarity to known binders" will get. You can use that number to help you guide your designs, but we're also interested in what novel designs you can come up with. If your similarity score tops out, switch your focus to something else (like the main score) and try to increase that.

Regarding the shared solution issue, we'll take a look into it: see also this feedback entry - If you have any additional info about the sharing issue, feel free to add it there.