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871b: De-novo Freestyle 36: Predicted Contacts
Status: Closed


Name: 871b: De-novo Freestyle 36: Predicted Contacts
Status: Closed
Created: 04/06/2014
Points: 100
Expired: 04/12/2014 - 23:00
Difficulty: Intermediate
Description: This is a follow-up puzzle for Puzzles 864 and 868, now with Predicted Contacts to help guide your folding. You can see the predicted contacts for this protein by clicking the Contact Map button in the Main menu (Selection Interface) or in the Actions tab (Classic Interface). You will notice that different contacts are shown in different shades of blue, with darker blue contacts indicating stronger predictions. Please ignore the contact multiplier in this puzzle, which should remain at 1.00 for all folded solutions; in this puzzle, satisfied contacts contribute directly to the Stability score. Note that for this puzzle, you will NOT be able to load in your manual saves from previous rounds.
Categories: Overall, Prediction

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bkoep's picture
User offline. Last seen 45 min 30 sec ago. Offline
Joined: 11/15/2012
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Repost of 871

This is a repost of Puzzle 871, which erroneously allowed loading of solutions from previous De-novo Freestyle 37 puzzles.

Joined: 09/19/2011
Groups: None
"871b: De-novo Freestyle 36: Predicted Contacts"

Shouldn't this puzzle be titled "871b: De-novo Freestyle 36: Predicted Contacts", not "871b: De-novo Freestyle 37: Predicted Contacts"?

bkoep's picture
User offline. Last seen 45 min 30 sec ago. Offline
Joined: 11/15/2012
Groups: None

Sorry, thanks for pointing that out CheezWhiz!

Susume's picture
User offline. Last seen 1 hour 57 min ago. Offline
Joined: 10/02/2011
Comments from chat about how this puzzle works

bkoep: Contacts are actually being scored as constraints in this puzzle, so the scoring mechanism for contacts is completely different from the visualization.
auntdeen2: ? then what good is the visualization? a semi loose guide?
bkoep: We still wanted you to have access to the "contact map"
bkoep: And the constraints match the contacts shown on the map
bkoep: Well, the constraints have different weights, for one, which shows up nicely in the map
bkoep: And the map might also be useful for inferring other information (such as the extent and placement of secondary structure units)
Susume2: the scores are the same when the contact is red as when it is green in the same position
bkoep: Okay, that makes sense.
auntdeen2: so we can't trust the color to know if we have made the contact?
bkoep: In this puzzle, it's less important to "make" the contact, because it isn't scored as an all-or-none bonus
bkoep: As two contacts get closer together, they score more and more points (up to some threshold)
bkoep: The color of the contact band does not reflect the score contribution of the contact
bkoep: this is analagous to how Rosetta approaches contacts, so we wanted to try it out
bkoep: It's worth noting that since the contacts are not scored as "bonuses" but contribute to the normal Stability score, wiggle will actually help you make the contacts if you're close enough.
Susume2: so they are sticky like the ED map is sticky
bkoep: So I would recommend relying on the map and contact visualizations only for large-scale planning and placement of SS elements
bkoep: @Susume, YES, exactly

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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, RosettaCommons