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687: 76 Residue Monomer Repost
Status: Closed

Summary

Name: 687: 76 Residue Monomer Repost
Status: Closed
Created: 03/14/2013
Points: 100
Expired: 03/21/2013 - 01:00
Difficulty: Advanced
Description: We are giving you a single chain of 76 residues to design. You will need the latest version of the client to play this puzzle There are 4 filters enabled in this puzzle. They are slow to compute, so you may want to check "Disable slow filters" in the behavior tab for when you are manually pulling and running your scripts. The ResidueIE filter ensures PHY, TYR, and TRP residues are scoring well. The "Core Exists" filter ensures the number of residues in the core is between 30% and 70%. The "Polar Core" filter that the residues in the core are properly hydrophobic. The "Layer Design" filter looks at the interactions of the residues based on the surface area of the protein. Residues can be either in the core, on the boundary or on the surface of the protein. Depending on the surroundings, the "Layer Design" filter will give you a bonus if your amino acid matches what it was expecting. Press TAB on each residue to find out more about these filters. You will not be able to load in your solutions from 676. Because of issues with the filters in that puzzle, we wanted to get a fresh start with these new filters. If everything goes well, nearing the end of this puzzle we will post a 76 residue symmetric dimer puzzle where you will be able to load your solution from this monomer into the dimer. Keep that in mind when you are designing your monomer.
Categories: Design, Overall

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Comments

Joined: 12/06/2008
Groups: Contenders
Beware the Disable slow filters

Howdy, y'all.

While the management says you can use the "Disable slow filters" checkbox on the Behavior slider, you need to know that running a mutate script while the filters are disabled will almost certainly cause the script to substitute sidechains that would be unacceptable when the filters are on. The end result will likely be a LOWER score than before you started.

The filter disabling shouldn't affect any rebuild, Quake variant, or sidechain-flipper scripts. But keep the filters enabled while mutating, else you will inadvertantly learn some new curse words.

Susume's picture
User offline. Last seen 3 days 18 hours ago. Offline
Joined: 10/02/2011
more on disabling filters

As I found on 682, even a wiggle or a rebuild that gains points with the filters disabled can result in a net point loss when they are re-enabled. This is because wiggles or rebuilds can cause parts of the protein to be slightly more or less hidden. This can cause your ratio of core to surface to change; it can cause individual residues to switch from core to boundary or boundary to surface; being in a new zone can change the list of what amino acids are allowed for that residue. All of these kinds of changes can lead to penalties (or in theory to bonuses), which you won't see until filters are switched back on. So leave some time to try and fix filter issues that might arise after any actions you take with filters off.

Joined: 12/06/2008
Groups: Contenders
I stand corrected.

Susume is correct! It didn't occur to me that slight movements of the backbone and sidechains using Quake variant scripts could move the classification of a residue from core to boundry or boundry to surface.

But the premise remains the same: don't blindly assume all will go well without the filters in place.

steveB's picture
User offline. Last seen 2 years 42 weeks ago. Offline
Joined: 01/08/2009
Groups: Void Crushers
Real world protein

Out of interest, I looked in the protein database for a protein of 76 residues and found ubiquitin. I hand mutate all of the residues to the correct amino acids, and then jmol to view the pdb model in 3D and then copied it through visually to foldit.

After working on it so that it was a close conformity, then compressed and run an automatic segment rebuilder on it, it has a grand score of 8498 pts, and the current top score for the puzzle is 10092 !

On this fold, the filters are giving -64,-240,-100 and -202

Mutating changes numerous side chains and ups the score to 8863.

I would expect a copy of a real world protein to outscore the top score by hundreds of points.

What is the take on this from foldit central, because from where I am looking something looks seriously wrong.

gitwut's picture
User offline. Last seen 32 weeks 4 days ago. Offline
Joined: 05/18/2012
Groups: Contenders
Tabbed segment Layer Design show same residue twice

I'm not sure why, but segment 26 when tabbed show HIS under Layer Design twice. I haven't noticed this on any other tabbed segments yet, though I haven't looked at them all.

tamirh's picture
User offline. Last seen 6 years 9 weeks ago. Offline
Joined: 05/11/2012
HIS twice

There are two variations of HIS. In the TAB list, it only uses the 3 letter name so you can't see that difference.

alwen's picture
User offline. Last seen 2 weeks 4 days ago. Offline
Joined: 10/03/2011
Polar? Hydrophobic?

This is like learning the whole game over again, and maybe writing a sonnet with AA abbreviations simultaneously.

I'm realizing I don't understand what FoldIt means by polar and hydrophobic, or what a core is.

tamirh's picture
User offline. Last seen 6 years 9 weeks ago. Offline
Joined: 05/11/2012
New terms

alwen, I don't think we have done a good job of introducing these new terms in a consise and organized fashion. I will write up a blog post that summarizes the new terms that the filters use and post it before the next symmetry puzzle goes up.

utaca's picture
User offline. Last seen 15 weeks 1 day ago. Offline
Joined: 01/18/2012
Groups: Void Crushers
Excuse me, i wouldn't vote

Excuse me, i wouldn't vote you down tamirh. It isn't a good idea to use this small arrows on an ipod without extending them.
I think this blog will be fine. ARROW UP!!!

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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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