/SEALContests are different than the science puzzles in Foldit.
The key differences are that contests:
- are created by Foldit players (not the Foldit science team)
- can run for a very long time
- require players to join
- may involve large proteins
- don't award global points
Contests are used for variety of purposes:
- competition for a group of students
- testing recipes
- testing new strategies
Creating a contestEdit
Contests are based on existing Foldit puzzles. There's a fixed list of puzzles that can be used when creating a contest. Some of these puzzles have specific proteins, with a fixed primary structure and a specific starting pose.
To create a contest, go to Add Contest on the Foldit web site.
Give the contest a name and a description, and select one of the available puzzles from the list. Finally, pick a start date and an end date for the contest.
Finally, click "Save" to create the contest.
When you have created a contest, you get a link to allow people joining it. You can share the link with others to allow them to join the contest. The contest can also be found on the Contests page on the Foldit web site.
As the creator, you have control over the contest. This allows you to delete the contest. You can also delete users or groups from your contest. Please use these powers for good. Being able to delete the puzzle is good if you accidentally select the wrong protein.
When you create a contest, please make it clear in the description if you want only certain players to join. If others do join, you can delete them from the contest if desired. Sending the deleted users a message via the Foldit site would be a nice touch if you do go this route.
Using a custom amino acid sequenceEdit
Contests use one of a fixed set of puzzles. There's no way create a contest using your own protein in a custom pose.
It is possible to copy an amino acid sequence (the primary structure) and apply it when playing an existing design contest. This doesn't give the protein a shape, but it does give you a starting point.
To apply a custom amino acid sequence, create a contest using the "Freestyle Design: Variable Length" puzzle. (Or check existing contests, there are likely one or more that are based on this puzzle.) The protein in this puzzle starts with 55 residues, but you can add or delete residues as desired.
Open the contest in Foldit, and adjust the protein to the desired number of residues.
The recipe AA Edit 1.2 can be used to copy and paste an amino acid sequence from another Foldit puzzle or an outside source.
These recipes represent the amino acid sequence as a series of one-character amino acid codes. Online sources such as the Protein Data Bank use the same format, known as FASTA format. You can copy and paste a FASTA-format sequence into the recipe, just don't copy the header information that sometimes appears in FASTA files.
Here's an example of a FASTA file:
In this case, ignore the header line, just copy the second line, "RPDF..." then paste it into the AA Edit recipe.
The recipe print protein 2.48 also provides the amino acid sequence (and much more) is copy-and-paste form.
The only constraints is that the players should never use the mutate function (which is embedded in many recipes) in order to respect the sequence given by the author of the contest. If this occurs by accident, it's always possible for the author to delete the unwanted player solution.
As in a Foldit puzzle, contest players can share solutions with members of their groups. For something like a class project, this means that one player could set the amino acid sequence and then share with the group. This would let others to start the contest with the desired sequence, sparing the effort of copying and pasting the sequence.
Using Foldit standaloneEdit
Outside of the normal structure of Foldit puzzles and contests, there's a standalone version of Foldit. The standalone version must be licensed by the University of Washington. See Foldit Standalone for more information.
The standalone version allows you use Foldit tools on any protein defined by a PDB (Protein Data Bank) file. This eliminates the restrictions of Foldit contests.
This tech note is from an early version of this page. It's not clear whether it's still valid:
- The Rosetta component can only read PDB files that start with ATOM records. Foldit standalone may crash if you try loading a PDB file with other records at the beginning, such as one downloaded from rcsb.org. Edit the PDB file, emove everything before the ATOM records, then try loading this modified version of the file.
List of contest puzzlesEdit
Currently, when you create a contest, you must select one of the following puzzles:
|Freestyle Design: Variable Length||This freestyle puzzle has mutable residues and allows you to add or delete residues, with a maximum of 100 residues.|
|Freestyle Design 20||A 20 segment designable extended chain.|
|Freestyle Design 40||A 40 segment designable extended chain.|
|Freestyle Design 80||An 80 segment designable extended chain.|
|Freestyle Design 100||A 100 segment designable extended chain.|
|Freestyle Design 150||A 150 segment designable extended chain.|
|Freestyle Design 200||A 200 segment designable extended chain.|
|Freestyle Design 500||An 500 segment designable extended chain.|
|Freestyle Symmetric Design: 40 Dimer||Two symmetric chains, 40 designable segments.|
|Freestyle Symmetric Design: 40 Trimer||Three symmetric chains, 40 designable segments.|
|Freestyle Symmetric Design: 80 Dimer||Two symmetric chains, 80 designable segments.|
|Freestyle Symmetric Design: 80 Trimer||Three symmetric chains, 80 designable segments.|
|HIV protease||HIV replication depends on HIV protease, a protein-cleaving enzyme which is the target for protease-inhibitor drugs.|
|GTPase Ras||The conformational change occurring in the small GTPase Ras is extremely important for the molecular basis of many cancers. The GTP-bound conformation of this protein should be in an ON state, signaling cell growth. Can you help it find this native fold?|
|Seal Myoglobin||This multistart puzzle has 8 different server models. See seal myoglobin for details. The protein appears to come from Ruminococcus gnavus, a bacterium, and not a seal.|
|Contest Template Test||A test contest with 166 residues.|
|Multi-Start Bacteroides Vulgatus Contest||Here are 5 server models. Resetting the puzzle will cycle through these 5 Zhang server predictions. They are also in the Alignment Tool so you can use partial threading as well as an extended chain.|
|Server models for T0743 Contest||Here are 8 server predictions for this CASP10 target whose native still hasn't been released. Resetting the puzzle will cycle through 8 different server predictions and they are available in the Alignment Tool so you can use partial threading between them.|
|Frizzled Design Puzzle Contest||The Frizzled protein occurs in a number of forms. We are giving you a form of Frizzled with a wide pocket. There are a couple of rules: You can mutate any residue on the helix but none on Frizzled and the small binding helix must stay in helical shape.|
|Nanog Transcription Factor||Introduction of Nanog into skin cells can help convert or 'reprogram' them into a state that is more stem cell-like. Solving this protein structure will help us design drugs that can activate Nanog and its binding partners as a strategy for patient-specific tissue regeneration. Resetting the puzzle will cycle through 5 Zhang server predictions that are also in the Alignment Tool so you can use partial threading.|
|Abeta Binder Piecewise Design||This is a different type of design puzzle from those you are most familiar with. Instead of designing a single long chain, here you can design a set of short peptides as disjointed sections of a larger protein—we don't want you to worry about designing connections between the short chains in this puzzle. See the new blog post about this for more information. The Abeta protein backbone is frozen in this puzzle, but there are eight short chains that you can completely redesign. This puzzle also includes a Residue IE filter, which monitors that all PHE, TYR, and TRP residues are scoring well.|