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652: 40 Residue Symmetry Dimer Retry

Closed since over 13 years ago

Advanced Overall Design Symmetry

Summary

Created
November 13, 2012
Expires
Max points
100
Description

This is a small (40 residue) symmetric dimer design puzzle. It is the same as 617 except there are two new features added to create better designs. The Residue IE (Interaction Energy) filter will give a bonus or penalty based on how well your residues are scoring compared to expected values. The LayerDesign filter will restrict the types of amino acids to encourage more realistic designs. A symmetric protein relies not only on how well folded each part is, but also on how well they interface together; see the latest blogpost about this: http://fold.it/portal/node/993871

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Comments

BootsMcGraw Lv 1

The filter will not allow me to place hydrophobes anywhere on a helix. I want to place hydrophobes in the area between two helices (the "inside"), while keeping the area to the outside of both hydrophilic. But no matter where I try to mutate a helix, it never lets me choose a hydrophobic, because all parts of a helix are apparently "outside".

I don't want to mutate my protein before I place it in some type of organized structure(s).

Am I doing something wrong, here? I am hearing cries like mine throughout chat. I really think the devs ned to re-consider how this filter works, or even if it we need it.

How about scoring "proper" sidechains better, but allowing us to mutate to whatever we think best?