bkoep's picture
User offline. Last seen 16 hours 58 min ago. Offline
Joined: 11/15/2012
Groups: None
Objectives

Core Existence: Monomer (max +3000)
Ensures that at least 30 residues are buried in the core of the monomer unit.

Core Existence: Complex (max +3700)
Ensures that at least 74 residues are buried in the core of the entire 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.

Secondary Structure (max +500)
No more than 50% of residues may form helices. Extra helices are penalized at 10 points per residue.

Joined: 06/24/2008
Groups: Void Crushers
Ideal Loops

The symmetry chain is lighting up as bad.

stomjoh's picture
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Joined: 11/18/2012
Groups: None
Too MANY Residues in the complex core?

If you want exactly 74 residues in the complex core, just say so. Anything under 74 is a point reduction - got it.
But you're also penalizing points for having more than 74 residues in the complex core???

bkoep's picture
User offline. Last seen 16 hours 58 min ago. Offline
Joined: 11/15/2012
Groups: None
Share with scientists?

Whoa, that's not right. None of these objectives should penalize you for having too many core residues. Can you share your solution with scientists?

Also, are there any details about the Objective penalty (if you hover your cursor over the Objective description)?

Joined: 03/05/2015
Groups: Gargleblasters
I got that too.

If I can replicate I'll share. I had fixed a bad loop and when it wiggled out too many residues in the core penalty came up. I noticed that penalty last night too when I was folding the pattern.
Shared solution. Hover says "Too many residues in the core. Move core (orange) residues out to the surface (4 to go)"

It appears to penalize 20 points per "extra" residue.

stomjoh's picture
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Joined: 11/18/2012
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I will try to replicate

But I trashed that design and started over.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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