I believe that this was tried last summer as a puzzle, but if there is enough demand for such a puzzle we can easily provide one.
I think the only reason we have not posted an extended chain conformation was that it might frustrate many players.
Hopefully Foldit now has enough tools to properly fold up a protein from scratch, and the Quest to the Native puzzles will have given everyone examples of what native proteins looks like.
I will bring this up at our weekly meeting if this is something that the Foldit community wants to try out!
we now have a puzzle starting from a fully extended chain!
http://fold.it/portal/node/986655
we hope you all enjoy it!
maybe we can release de-novo CASP targets this way (targets where there are no similar solved structures to use as a template)
I like the idea of not having a preconceived notion of what the folded protein should look like but I think being given the protein in a straight line is overdoing it. I'd prefer to see the secondary structure given as Madde originally suggested: either that or, as has been done in some all-hands puzzles, give players the choice of selecting one of several initial candidate structures.
Nicky, the wiggle won't take it to a regular pre-folded structure necessarily because the protein won't have any mojo at all. Mojo causes proteins to revert to their original state after a a change has taken place.
I believe that this was tried last summer as a puzzle, but if there is enough demand for such a puzzle we can easily provide one.
I think the only reason we have not posted an extended chain conformation was that it might frustrate many players.
Hopefully Foldit now has enough tools to properly fold up a protein from scratch, and the Quest to the Native puzzles will have given everyone examples of what native proteins looks like.
I will bring this up at our weekly meeting if this is something that the Foldit community wants to try out!
No, the wiggling wpould not make the protein to a shape.
infjamc did it on one of the last puzzles, he did a 100% helix structure in one line - and even scored quite good with this. ^^ Very interesting. I played around with it a bid and it didn't revert to a normal structure at all.
I would like the idea - but give it enough time!
We could have an intro that explains how to fold a protein from scratch. Like a small protein that would be easy to fold could be used as an example.
we now have a puzzle starting from a fully extended chain!
http://fold.it/portal/node/986655
we hope you all enjoy it!
maybe we can release de-novo CASP targets this way (targets where there are no similar solved structures to use as a template)
I like the idea of not having a preconceived notion of what the folded protein should look like but I think being given the protein in a straight line is overdoing it. I'd prefer to see the secondary structure given as Madde originally suggested: either that or, as has been done in some all-hands puzzles, give players the choice of selecting one of several initial candidate structures.
Thanks for the quick feedback!
We have implemented your suggestion in the next freestyle puzzle that is being released today (it's the next blind mini-CASP target).
The reason we didn't assign any secondary structure (and in certain past Foldit puzzles we have given you no secondary structure assignment) is because those aren't necessarily correct.
Secondary Structure Prediction used to have its own category at CASP, and there are many difference methods for predicting the secondary structure of an unknown protein:
http://www.bmm.icnet.uk/people/rob/CCP11BBS/secstrucpred.html
It is a lot more accurate than tertiary structure predictions, but it is still not exact (especially with difficult targets) so we don't want players thinking that the secondary structure is set in stone and shouldn't ever be changed!
Hopefully for the Mini-CASP 2-Freestyle puzzle you will all use the secondary structure assignment as a recommendation!
