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tamirh's picture
User offline. Last seen 8 years 19 weeks ago. Offline
Joined: 05/11/2012

The Residue interaction energy bonus is a comparison of the residues in your protein versus those of a large set of native proteins.

We take a subset of score terms that have to do with residue-to-residue interactions and give each residue a combined score. We see how well your amino acid stacks up against others of the same type in the set of native proteins we scored. We do this across the entire protein and determine a bonus or penalty.

This will give penalties when residues are not contributing at a proper level. In essence, is this residue pulling its weight based on what we have seen it capable of doing on average.

If you are in-game and have a penalty, you can expand the bonuses list and click on "Show" to see which residues are contributing most to your penalty. The larger/darker the red (default color) circles the more of an influence that residue is having.

Let me know if any of this wasn't clear of if you have questions at all. I'll try and answer or find the right person to answer them.

Note:
There's a bug currently where the game will say "All bonuses gained, no conditions" even if you have a penalty.

marie_s's picture
User offline. Last seen 1 year 28 weeks ago. Offline
Joined: 05/18/2008
Groups: None
the residue contribution

the circles arent a little too large?
http://fold.it/portal/files/chatimg/irc_33153_1348691242.png

tamirh's picture
User offline. Last seen 8 years 19 weeks ago. Offline
Joined: 05/11/2012
Yes, I wasn't restricting the

Yes, I wasn't restricting the size of the glow so if the energy level was very far off the size would grow to larger than the protein itself. The next devprev this will be fixed.

A better explanation of what's actually happening from David Baker:

The main purpose of this new addition to prevent unrealistic residue substitution in Foldit. For example, it makes adding tryptophans, tyrosines, and phenylalanines on the surface of a protein score poorly. Putting hydrophobic residues on the surface is bad because it makes the protein very "sticky", likely to interact with many other proteins, including itself, and hence not very useful.

Joined: 12/06/2008
Groups: Contenders
More colors... ugh.

I want to suggest adding the actual scoring data to the "show" section as an option. Trying to figure out the relative size of a hazy red circle is overwhelming when the protein is already too busy with its myriad shapes and colors.

Yes, I am colorblind, but this is a "too much information presented at once" issue. Keep it simple. Just let me see the numbers, please.

Joined: 06/17/2010
Segment score (number) on each segment?

Neat idea :)

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