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1725: Symmetric Trimer Design: 80 Residues
Status: Closed

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bkoep's picture
User offline. Last seen 20 hours 19 min ago. Offline
Joined: 11/15/2012
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Objectives

Core Existence: Monomer (max +2400)
Ensures that at least 24 residues are buried in the core of the monomer unit.

Core Limit: Complex (max +500)
Checks that no more than 87 residues are buried in the symmetric complex, including the interface between monomer units.

SS Design (max +500)
Penalizes all CYS residues. Penalizes GLY, ALA residues in sheets. Penalizes GLY, ALA, SER, THR in helices.

Ideal Loops (max +500)
Penalizes any loop region that does not match one of the Building Blocks in the Blueprint tool. Use "Auto Structures" to see which regions of your protein count as loops.

Batz's picture
User offline. Last seen 2 days 17 hours ago. Offline
Joined: 02/16/2012
Groups: Go Science
Core Limit filter

Just for understanding:

Does this mean that the Core Limit filter is the highest if the monomers do not touch at all?
Or is there still the Core Existence filter included?
If not I assume players will rather design three monomers floating around instead of proper trimers :D

Thanks

bkoep's picture
User offline. Last seen 20 hours 19 min ago. Offline
Joined: 11/15/2012
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No Core Existence for Complex

That's right, the only requirement of the Core Limit: Complex objective is that fewer than 87 residues are buried in the core. As far as the objective is concerned, it is perfectly okay to have three floating monomers that are too far apart to interact.

However, we expect that players will be able to get more points by bringing those monomers close into contact with one another, in a well-packed trimer.

Batz's picture
User offline. Last seen 2 days 17 hours ago. Offline
Joined: 02/16/2012
Groups: Go Science
That's really

That's really interesting!
Esp. when checking how much less the designed trimer scores when its actually a monomer (with redesigned sidechains).

Thanks :)

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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, Amazon, Microsoft, Adobe, RosettaCommons