beta_helix's picture
User offline. Last seen 1 day 52 min ago. Offline
Joined: 05/09/2008
Groups: None
Screenshot of the template used for this starting model

To give you an idea of what one of the possible templates looks like:

.

We believe that this CASP target might have a very similar fold.

beta_helix's picture
User offline. Last seen 1 day 52 min ago. Offline
Joined: 05/09/2008
Groups: None
Additional info about this CASP target

Here is the CASP link for this target (showing the amino acid sequence):
http://predictioncenter.org/casp10/target.cgi?id=77
____________________________________________________

Here is the sequence logo predicted by the SAM server.

H = helix
E = sheet
C = loop (or coil)

The taller the letter at each position, the higher the probability of that specific secondary structure for that amino acid.

You can see that this protein is pretty much predicted to be helical, with residues 49-115 predicted to be one long helix!

More info on coiled coils: http://en.wikipedia.org/wiki/Coiled_coil

Joined: 08/30/2011
if the letter isn't that big,

if the letter isn't that big, is it more possible that the helix is bended there?

beta_helix's picture
User offline. Last seen 1 day 52 min ago. Offline
Joined: 05/09/2008
Groups: None
It could mean there is a break in the helix

Instead of having one long helix, it could actually be a helix bundle: helix-loop-helix-loop-helix as opposed to one long helix.

You'll be able to see that with the next T0680 puzzle, as that is one of the "other topologies" mentioned in the puzzle description.

__________________________________________

If you want to look at even more predictions for this target, you can look at ALL the SAM-T08 results for T0680:
http://compbio.soe.ucsc.edu/SAM_T08/results/target08-query-1337702652-9633/summary.html

You can read Part 6 here to understand what everything means:
http://compbio.soe.ucsc.edu/SAM_T08/faq.html

But, for example, if you look at the alpha predictions:
http://compbio.soe.ucsc.edu/SAM_T08/results/target08-query-1337702652-9633/T0680.t06.alpha-logo.pdf

...it does look like it could be 3 helices instead of one long one, but there is no way to know for sure until they solve the structure!

User login
Download links:
  Windows    OSX    Linux  
Windows
(7/8/10)
OSX
(10.12 or later)
Linux
(64-bit)

Are you new to Foldit? Click here.

Are you a student? Click here.

Are you an educator? Click here.
Social Media


Search
Only search fold.it
Other Games: Mozak
Recommend Foldit
Topics
Top New Users
Sitemap

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