Bands made by Contact Map in Puzzle 883 are between alpha-carbons

Case number:845813-997623
Topic:Game: Tools
Opened by:jeff101
Status:Open
Type:Question
Opened on:Monday, May 5, 2014 - 04:29
Last modified:Tuesday, May 6, 2014 - 06:00

It looks like in Puzzle 883, bands made using the Contact Map all form with strength 1 and length 3.5 Angstroms between alpha-carbons for the segments of the contact. You can tell if you view them with CPK, stick, and show stubs or show all sidechains. Forming bands between alpha-carbons seems odd considering the many comments made by bkoep in http://fold.it/portal/node/997478#comment-27181 about beta-carbons and Contact Maps. Is the Contact Map in Puzzle 883 behaving as desired?

(Mon, 05/05/2014 - 04:29  |  4 comments)


jeff101's picture
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p.174 of the paper at http://dx.doi.org/10.1016/j.jbi.2011.10.008 says "According to CASP, two residues are considered to be in contact when the 3D physical distance between their C-beta atoms (C-alpha for GLY) is below a threshold value of 8 Angstroms." Is this the rule that Foldit uses to determine which boxes in the Contact Map have black dots in them?

bkoep's picture
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Currently, we use beta-carbon distances to evaluate contacts; however, bands made with the contact map are formed between alpha-carbons. The main reason for this is that we wanted to get the new Contact Map released as soon as possible, and the banding discrepancy didn't seem critical to function.

In the future, we plan to update the Contact Map so that these bands are formed between beta-carbons. The length of the band may be dependent on the types of residues involved, and the strength of the band may depend on the strength of the contact prediction.

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Thanks for the clarification.

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So I take it that the answer to my question above (see http://fold.it/portal/node/997623#comment-27522)about the black dots in the Contact Map is "yes". Is this correct?

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