puzzle picture
1024: 75 Residue Monomer Design: Zero Cysteines
Status: Closed

Summary

Name: 1024: 75 Residue Monomer Design: Zero Cysteines
Status: Closed
Created: 12/11/2014
Points: 100
Expired: 12/18/2014 - 23:00
Difficulty: Intermediate
Description: In this puzzle, we're asking players to design a protein with no cysteine residues! Remember that the SS Design filter now considers the environment around each residue, in addition to secondary structure. This means that some residue types will be restricted depending on whether the position is in the core or surface of the protein. There are several other filters in effect; see the puzzle comments for 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!
Categories: Design, Overall

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Comments

bkoep's picture
User offline. Last seen 41 min 5 sec ago. Offline
Joined: 11/15/2012
Groups: None
Filters

Residue IE Score: Monitors that all PHE, TYR, and TRP residues are scoring well.

Core Existence: Ensures that at least 30% of the residues are buried in the core of your design.

Fragment Score: Scans for parts of your design that are unlikely to fold up naturally. Use Rebuild and Remix tools to fix these regions of your design!

Secondary Structure: Checks that no more than 50% of residues are in helices; penalties are incurred if more than 50% of residues form helices.

Secondary Structure Design: Penalizes all CYS residues. Penalizes GLY, ALA, and PRO residues in helices and sheets. Also penalizes hydrophilic residues in the core and hydrophobic residues on the surface.

Joined: 10/30/2012
Groups: Beta Folders
any chance of modifying the

any chance of modifying the mutate function, rather than having to go back and do it by hand each time one uses it.

bkoep's picture
User offline. Last seen 41 min 5 sec ago. Offline
Joined: 11/15/2012
Groups: None
On the docket

You mean, modify the mutate function so it adheres to filter rules?

Sometimes the Mutate function does make a mutation that causes a filter to fail; I agree this behavior is undesired and also inefficient. This fix is high on the to-do list, and hopefully will be added soon.

spmm's picture
User offline. Last seen 4 weeks 1 day ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
still penalising gly in loops

gly in the loops between sheets is getting penalised.

bkoep's picture
User offline. Last seen 41 min 5 sec ago. Offline
Joined: 11/15/2012
Groups: None
Share with Scientists

Could you share this solution with us, so I can take a closer look?

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Microsoft, Adobe, RosettaCommons