Foldit Puzzles

1465: Revisiting Puzzle 144: Rosetta Decoy 8

This is a throwback puzzle to the early days of Foldit. The function of this thermophilic protein is unknown, but it is unusual among intracellular proteins in that the native structure includes disulfide bonds. This protein contains six cysteine residues that are oxidized to form three disulfide bonds. We are revisiting old Foldit puzzles so we can see how useful the recent additions to the game have been.

1464: Medium Monomer Design

This puzzle challenges players to design a single-chain protein with 75-90 residues. We've softened the penalties associated with the Core Existence filter, which have typically been very steep. The starting structure has 75 residues, but more can be added at a cost of 16 points per residue. See the puzzle comments for filter details. The Baker Lab will run folding predictions on your solutions for this puzzle, and those that perform well will be synthesized in the lab. Remember, you can use the Upload for Scientists button for up to 5 designs that you want us to look at, even if they are not the best-scoring solutions!

1462: Reindeer Beta-lactoglobulin

This protein is a component of reindeer milk. Beta-lactoglobulin is a protein found in the milk of many mammals, including cows and sheep, but not in humans. Its natural function is still unknown. The structure of this protein was determined (with some difficulty) by x-ray crystallography in 2006. However, parts of the published structure are a little bit problematic. We want to see if Foldit players can fold this protein starting from an extended chain. Secondary structure predictions (from PSIPRED) are marked on the starting structure, and provide clues about where the protein might form helices and sheets! Note that, due to the large size of the protein, this puzzle will be active for two weeks.

1463: Classroom Puzzle: HIV RNA

In this Classroom puzzle, students will learn about RNA structure and dynamics, as well as the ongoing debate between conformational capture and induced fit models of biomolecular binding. The RNA molecule of choice here, HIV TAR, is provided in one of its many possible folded conformations. However, we know the RNA is flexible, and it is still unclear what fold is most favorable for this molecule. See if you can find other stable folds for this RNA molecule!

1460: Large Monomer Design

This puzzle challenges players to design a single-chain protein with 85-105 residues. We've softened the penalties associated with the Core Existence filter, which have typically been very steep. The starting structure has 85 residues, but more can be added at a cost of 16 points per residue. See the puzzle comments for filter details. The Baker Lab will run folding predictions on your solutions for this puzzle, and those that perform well will be synthesized in the lab. Remember, you can use the Upload for Scientists button for up to 5 designs that you want us to look at, even if they are not the best-scoring solutions!

1461: Revisiting Puzzle 143: Rosetta Decoy 7

This is a throwback puzzle to the early days of Foldit. This enzyme helps to regenerate a cofactor that is necessary for nucleic acid synthesis; the starting structure is a model produced by Rosetta. This protein contains only one cysteine, so no disulfide bonds are expected. We are revisiting old Foldit puzzles so we can see how useful the recent additions to the game have been.

1459: Revisiting Puzzle 142: Rosetta Decoy 6

This is a throwback puzzle to the early days of Foldit. This protein was evolved in vitro to bind testosterone; the starting structure is a model produced by Rosetta. This protein contains two cysteine residues, which oxidize to form a single disulfide bond. We are revisiting old Foldit puzzles so we can see how useful the recent additions to the game have been.

1458: Small Monomer Design

This puzzle challenges players to design a single-chain protein with 65-75 residues. We've softened the penalties associated with the Core Existence filter, which have typically been very steep. The starting structure has 65 residues, but more can be added at a cost of 16 points per residue. See the puzzle comments for filter details. The Baker Lab will run folding predictions on your solutions for this puzzle, and those that perform well will be synthesized in the lab. Remember, you can use the Upload for Scientists button for up to 5 designs that you want us to look at, even if they are not the best-scoring solutions!

1455: Aflatoxin Challenge: Round 4 with Insertions

This is the fourth puzzle of our Aflatoxin Challenge; now players may insert and delete residues in solutions from the previous Round 3 puzzle. Aflatoxins are a class of poisonous compounds that contaminate a significant portion of the global food supply. In this puzzle, players are challenged to redesign an enzyme that could break down aflatoxin molecules. The majority of the protein is frozen, with the aflatoxin ligand fixed in a binding pocket. Surrounding the binding pocket are a number of loops that might be redesigned without affecting the folding stability of the protein. In these loops, players may manipulate the protein backbone and mutate the residue sidechains. Players may add up to 20 additional residues within these loops, at a cost of 16 points per residue. Players may load in solutions from Puzzle 1450.

1457: Extra Large Monomer Design

This puzzle challenges players to design a protein with 95-120 residues. We've softened the penalties associated with the Core Existence and Residue Count filters, which have typically been very steep. The starting structure has 95 residues, but more can be added at a cost of 16 points per residue. See the puzzle comments for filter details. The Baker Lab will run folding predictions on your solutions for this puzzle, and those that perform well will be synthesized in the lab. Remember, you can use the Upload for Scientists button for up to 5 designs that you want us to look at, even if they are not the best-scoring solutions!