Closed since over 9 years ago
Intermediate Overall Prediction Predicted ContactsNOTE: The expiration date for this puzzle has been extended by 1 week, due to the size and complexity of the problem.
This is a follow-up puzzle for Puzzle 1258, now with Predicted Contacts to help guide your folding! See the blog for information on using the contact map. 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 green, with brighter green contacts indicating stronger predictions. Players will be able to load in manual saves from Puzzle 1258 and use them as a starting point here. This protein is currently being investigated for drug discovery against Tuberculosis (TB), although its structure is still unknown.
Sequence:
http://foldit.wikia.com/wiki/Distance_Maps and http://memorize.com/distance-and-contact-maps show Distance and Contact Maps along-side their respective 3D images for many different proteins. Images are classified as in the SCOPe database (http://scop.berkeley.edu), and http://memorize.com/distance-and-contact-maps can shuffle the images in multiple-choice and matching modes to help you learn the patterns in them.
Could we please have two weeks on this puzzle? It is complex enough to require several days of hand work, possibly with multiple restarts, and large enough to require several days of running scripts. With the planned down time on top of that, you will not be getting everyone's best work.
My best score on 1258 was not my best work, but my first effort, because that was the only one I had time to run a full complement of scripts on. My best effort was a share-with-scientists version that never had time to reach its top score. I would hate to have the same thing happen with 1261.
Just for the info:
There are 302 predicted contacts with potentially 10027 points for them.
So based on the best piece of 1258: 9670 points.
The hurdle is at 19697 points…
Good Folding!!!
:)
Just a question. In case this protein is in lipid environment (at least partly, as I understood from discussion between Susume,jeff, Afligen etc), can we still trust the Roseta hiding subscore ?
Should it be deactivated in the Roseta calculation?
Hi Bruno,
The anchored portion of the protein that is in the lipid environment is removed and only the soluble portion is present in the current sequence.
As a side note, Foldit/Rosetta can handle lipid environments if the score function is modified; one day I hope to post a membrane protein, but for that, it would be important to visualize the lipid bilayer, which is currently not implemented.
Hi Susume!
The puzzle will be extended for a week. I will update the text on the description of the puzzle and extend the time. Thanks for letting me know about this.
Hi Everyone,
As mentioned in a previous comment for phase 1 of this puzzle, a paper to look at is:
"The bottom sequence in Figure 4 is M. tuberculosis LepB, and it’s aligned with the E. coli sequence (1st sequence). There’s a more recent review paper by Auclair et al (2012) with a similar figure, although in that one they refer to the M. tb protein as “Sip” instead of “LepB”."
Hope that helps out!
The fig 4 shows an alignment with e.coli. My problem is that I cannot interpret this (or do we have to find the related 3D picture portion of E.Coli on internet?). Should it be available with an alignment tool? Or would it be useful if yo post a picture of this portion here?
of solved box B;, box C etc … with the related segment numbers in our puzzle - that would be great for a visual copy
Is the following the Auclair et al (2012) review article mentioned above?
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3323777/
Thanks!
