Foldit participating in the WeFold CASP 10 project
For the first time in CASP's 18 year history, a handful of labs worldwide have decided to combine forces for a "Collaborative group initiative": http://www.wefold.org/
Since Foldit was the first truly global collaborative structure prediction team at CASP9, we are proud to be part of this new WeFold project.
Other groups will be sharing their templates, alignments, secondary structure and contact predictions, constraints and models with us to post as Foldit puzzles, and we will be sharing your predictions with other groups for them to score using different energy functions than Rosetta, cluster and even refine.
Any final model generated using this collaborative approach will be submitted by the WeFold CASP 10 team (denoting which methods were used at each step, Foldit being one of these) and is independent from our Foldit Group submissions (which are exclusively generated by you).
Here is a list of participants:
http://wefold.files.wordpress.com/2012/03/wefold-table.pdf
with more info on the WeFold website: http://www.wefold.org
beta_helix 170 3295 |
Sat, 05/12/2012 - 21:22 |
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New Symmetric Beta Core Design Puzzles
Structured dimeric and trimeric peptides are great starting points for a major bioengineering challenge.
Specifically, they can be used as building blocks for designing useful, rigid assemblies of proteins, like crystals and nanocages. The smallest such starting point for this kind of design is an ...WXCXW... motif, which forms a tiny structured homodimer: a short beta sheet stabilized by a cross-strand disulfide bond and two tryptophan/tryptophan interactions.
The only problem: this motif is so tiny, it is difficult to do anything with; it needs to be larger but retain rigidity. Otherwise anything goes: beta sheets, alpha helix docking, rigid loops, you name it.
We've given you 20 extra residues to play with on this first puzzle (http://fold.it/portal/node/992625) and can't wait to see what you can do!
The most viable looking of the top-10 high scoring structures will be made and characterized; we'll let you know how it turns out!
For more info & background about these puzzles, check out the transcript from my Scientist Chat:
http://fold.it/portal/node/992469#t15:18
DrLemming 170 8000 |
Wed, 05/09/2012 - 23:40 |
2 comments
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Seth Cooper wins the world's best computer science thesis award
Seth Cooper's PhD thesis wins the 2011 ACM Dissertation Award with his design and development of the Foldit scientific discovery platform.
http://www.acm.org/press-room/news-releases/2012/service-awards-2011
This is an amazing achievement for Seth. But more importantly, Seth, as well as the entire Foldit team, know that this is really your award because it is exactly the Foldit community and the expertise development that evolved over the past 4 years within the community that produced all exciting results.
Congratulations to you all,
Zoran
zoran 170 8000 |
Wed, 05/02/2012 - 16:37 |
9 comments
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The Alignment Tool: Purpose and Prospects
During protein evolution, amino acid sequences generally change faster than three dimensional structures. Evolutionarily related proteins almost always have similar structures, and hence to predict the structure of a protein it is very useful to identify proteins with similar amino acid sequences whose structures are known. The sequence of the protein of interest can then be "threaded" onto the known structure, which is referred to as the template. The resulting structure is a good starting point for additional refinement.
While automated methods can correctly choose the right template structure for very closely related proteins, when the sequences have diverged considerably during evolution identifying the correct template and aligning the sequences correctly (such that corresponding residues in the three dimensional structures are properly superimposed) can be quite difficult. Starting from the wrong template and/or the wrong alignment puts you that much further from the best scoring structure.
This is where the Alignment Tool comes into play. The Alignment Tool allows the user to hand thread a sequence over potential homologues, giving human spatial reasoning a chance to do what automated methods frequently can't. In addition, the alignment tool allows users to mix and match the best parts of each alignment into a hybrid template since different sequence alignment techniques have their strengths and weaknesses.
Bottom Line: In this year’s CASP, the new alignment tool offers players a potential edge over everyone else.
( Posted by beta_helix 170 3295 |
Mon, 04/30/2012 - 06:17 |
10 comments
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Preliminary results from Immunotherapy design puzzle (539)
Here are some preliminary results from the first Immunotherapy design puzzle (539). The results you generated were very interesting and we are still in the process of analyzing them. But to give you a glance at some useful structures we've posted a gallery puzzle where you can view them and play around.
In general 85% of the top-1000 scoring structures (as ranked by the Rosetta score) made use of the pronounced cavity between the two loops on the CTLA-4 protein. To give you some insight of the different binding modes a cool statistic to look at is the type of cavity residue. Looking at the type of cavity residues, there was a diversity between several hydrophobic residues as can be seen in this table:
Cavity residue Abundance
*TRP 30%
*PHE 29%
*TYR 22%
*MET 19%
This diversity helps us to obtain useful hits, since the solutions were not directed towards one species inside the cavity. We do not only consider the Rosetta Score (which is your only guide), we also evaluate the binding energy between the 3 amino acids and the protein and we consider the resemblance of the two partners with regard to their shape. This gives us an indication how well your solutions will bind CTLA-4 when we actually produce them.
In the gallery we present three interesting solutions you came up with:
Foldit Player JackWeaver's solution: http://fold.it/portal/node/992496
Foldit Player Mark-'s solution: http://fold.it/portal/node/992497
Foldit Player Flagg65a's solution: http://fold.it/portal/node/992499
We have posted a new Immunotherapy design puzzle:
http://fold.it/portal/node/992493#comment-16973
and will have a Scientist Chat to discuss it:
http://fold.it/portal/node/992505
EvdH 170 3566 |
Thu, 04/26/2012 - 23:55 |
2 comments
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