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652: 40 Residue Symmetry Dimer Retry
Status: Closed


Name: 652: 40 Residue Symmetry Dimer Retry
Status: Closed
Created: 11/12/2012
Points: 100
Expired: 11/22/2012 - 23:00
Difficulty: Advanced
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
Categories: Design, Overall, Symmetry

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tamirh's picture
User offline. Last seen 9 years 10 weeks ago. Offline
Joined: 05/11/2012

For more info on the Layer Design filter, please see: http://fold.it/portal/node/993855

Joined: 12/06/2008
Groups: Contenders
Not realistic at all!

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?

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, Boehringer Ingelheim, RosettaCommons