bkoep's picture
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Residue IE Score: Monitors that all PHE, TYR, and TRP residues are scoring well.

Core Existence: Ensures that at least 35% of the residues are buried in the core of your design.

Secondary Structure: Checks that no more than 50% of residues are in helices; penalties are incurred if more than 50% of residues form helices.

Secondary Structure Design: Penalizes all CYS residues. Penalizes GLY, ALA residues in sheets; penalizes GLY, ALA, SER, THR in helices.

Residue Count: Penalizes extra residues inserted beyond the starting 90. Players may use up to 125 120 residues in total.

LociOiling's picture
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120 segments maximum

The comments say 90 to 125 segments, but I can't add beyond segment 120. That's actually the normal maximum for an "extra large monomer", so we'll assume the 125 was a typo.

bkoep's picture
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You're correct, that was a typo. Thanks for pointing it out! I've amended the comment.

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Broken protein?

I was able to get my protein up to 9826, however after that point the system appeared to 'break'.

Any manner of wiggling other than local would force the protein to come apart and fold to a worse score with negative penalties for loops not scoring high enough and not enough residues in the core.

I tried low/medium power, with clashing importance adjusted from 0.03 to 1.00 - Same result every time.

bkoep's picture
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That's weird. Can you share your solution using the Share with Scientists button, and we'll take a look?

Susume's picture
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Remove blueprint constraints?

When a monomer design starts pulling radically out of shape, sometimes it means the "ideal loop" constraints have moved to the wrong spot on the protein due to deleting/adding segments. Open blueprint, and if there are white rectangles on the sequence of letters, drag the rectangles off. That removes the constraints and lets your protein wiggle more freely.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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