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2106: Design with Neural Net Objective

Closed since about 4 years ago

Intermediate Overall Design

Summary

Created
February 09, 2022
Expires
Max points
100
Description

Design a protein with the help of the new Neural Net Objective! The Neural Net Objective can help identify parts of your protein that should be mutated to improve AlphaFold prediction confidence. After you use the AlphaFold tool to get a prediction, click "Show Neural Net Objective" to color your protein based on local distogram analysis. To improve AlphaFold prediction confidence, try mutating residues that are colored red by the Neural Net Objective. Players should aim for an AlphaFold confidence and similarity of 80% or more.



We are especially interested to see what creative new folds players might come up with. There are no additional Objectives, but we expect successful designs will still need lots of helices or sheets, with short minimal loops, as well as a closely-packed core of orange hydrophobic residues. AlphaFold predictions will not affect your score. Players may insert and delete residues to a maximum of 120 residues total.

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Comments

BootsMcGraw Lv 1

My first attempt at a design gave a 52.6% confidence. When I clicked the "show neural net" option in the objectives, all 120 residues turn an identical shade of dark grey. Not one bit of red.

My design is awful. Why is the game telling me there is nothing to change?

Vincera Lv 1

For the past two hours or so, I've attempted (unsuccessfully) to upload to AF. My [circa] midnight uploads transmitted and rendered results but since this morning, nada. Are any other players experiencing this problem?

ichwilldiesennamen Lv 1

I have noticed in the last weeks that the amount of uploadable solutions to scientists is very limited. For this puzzle I can only upload 5 solutions. Is this intended? I would have more to share but I do get some message like "too many shared solutions…" I can upload many more to teammembers though. Is this a bug or a feature? I think this cropped up since AF was introduced but I am mot sure there.

bkoep Staff Lv 1

Yes, it looks like the AlphaFold server is currently down for everyone. We're looking into the issue.

bkoep Staff Lv 1

Yes, we currently limit AlphaFold submissions to maximum 5 pending requests at any time. Once a pending job completes, then you may submit a new job.

Since our AlphaFold server is currently down, pending jobs are not completing. Once we get the server back online and your pending jobs are completed, then you will be able to make new submissions. Apologies for the unexpected downtime!

bkoep Staff Lv 1

That is a little odd if everything is exactly the same shade, and may indicate a bug. Can you share this solution with scientists?

But there could be other cases where the AlphaFold confidence is very low, and the Neural Net Objective is completely lukewarm.

Many sequences are not expected to fold at all, and in the real world these will adopt an "intrinsically disordered" or "random coil" structure. In such cases, we would expect AlphaFold to predict a relatively featureless distogram, where every residue-residue distance is represented as a flat distribution (i.e. "the distance between these two residues could be anything"). Probably the AlphaFold predicted structure will be very loopy and loosely-packed.

In this case, the distogram cross entropy will not be good, but also it may not be especially bad. We might interpret this like AlphaFold saying, "I don't see any evidence that your design will fold into this structure, but also I don't see any evidence that it will fold into anything else."

ichwilldiesennamen Lv 1

I did not mean uploads to alphafold but instead the upload of a solution to scientists in the filedialog (where I could also upload to group or to myself). THIS is limited to 5 for me in shares to scientists. Or are the number of pending uploads to AF and the number of shareable solutions in filedialog coupled? I would find that strange.
Anyway, thx for trying to get the AF server back online. I will have to stall my investigations until it is available. Good luck in getting it back up again!

BootsMcGraw Lv 1

Yes, everything is exactly the same dark shade of grey. I'll share, next time I log into the game.

I think I may be experiencing a "1D10T" error. I really don't understand how to use this tool.

Okay, I upload my solution to AlphaFold and wait for it to spit out some percentages. What am I supposed to do, next? Can y'all please give us some training?