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422: De-novo Freestyle 7

Closed since almost 15 years ago

Advanced Overall Prediction

Summary

Created
May 21, 2011
Expires
Max points
100
Description

We are giving you this currently unsolved protein as an extended chain. Use all your skills to fold it up as best as you can. The secondary structure predictions are posted in the puzzle comments, but we have included them in the starting structure as well.

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Comments

beta_helix Staff Lv 1

As requested in the feedback, http://fold.it/portal/node/989298 these secondary structure predictions have been pre-loaded into this freestyle puzzle.

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.

For example, the amino acid Leucine at residue 20 is highly predicted to be part of a helix. However, the Leucine at residue 16 is equally predicted to be anything.

tyler0911 Lv 1

Why can't I see this in my list of puzzles?
Really want to get to work on this one…

spvincent Lv 1

One thing I've noticed in the high-scoring solutions I've seen for these de novo puzzles is that any sheets tend to be unnaturally straight. In real-world proteins (see the recently-completed 419 as an example) sheets are usually curved, but this is difficult to achieve in FoldIt, particularly when one starts with a perfectly straight sheet as happens in these puzzles.

A personal preference this; but I think trying to fold from a totally unfolded protein is too purist an approach. I'd rather have a few random Rosetta@home predictions to start from (you could use them to populate the Alignment tool).

bendbob Lv 1

I do not know about getting serve data for SS's. Any pointers and clues are appreciated.