puzzle picture
1035: Incredibly Difficult 95-residue Electron Density Design Puzzle
Status: Closed

Summary

Name: 1035: Incredibly Difficult 95-residue Electron Density Design Puzzle
Status: Closed
Created: 01/08/2015
Points: 100
Expired: 01/22/2015 - 12:00
Difficulty: Advanced
Description: This puzzle is unlike anything we have ever posted before! We have given you extremely accurate electron density, but no sequence information. This protein has 95-residues, but your starting model only has 5 Alanines that are floating in the density. You'll need to insert residues and mutate them as you make your way through the density. We know this won't be easy, some might even suggest that this task is impossible... but we know that if anyone can do it: you can! We are giving you two weeks to work on this... good luck!
Categories: Design, Electron Density, Overall

Top Groups

RankGroupScorePoints
1Gargleblasters25,273100
2Anthropic Dreams25,24584
3Go Science25,23770
4Void Crushers25,22057
5Herobrine's Army25,14847

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Comments

beta_helix's picture
User offline. Last seen 12 hours 7 min ago. Offline
Joined: 05/09/2008
Groups: None
We know this is going to be very different...

but we also hope it'll be fun!

There will obviously not be any secondary structure predictions or any additional information for this puzzle.

__________________________________________

Cutaway view hint:
If you hover your mouse over a segment and type shift-Q, the game will hide parts of the protein and cloud that are not in the same plane as that segment - it cuts down on how much cloud you see at one time and makes it easier to focus. Q returns to normal view.

__________________________________________

Electron Density Features:

- Notes can be added to the electron density if present. To add one, press TAB with the mouse over the density while the density panel is open. Use the recycle button in the note panel to erase one.

This video from our YouTube channel has Seth Cooper explaining how to add Notes to the electron density: http://youtu.be/iaVk8Yo0_MA

- There is a button in the Electron Density Panel to focus rotation on the density. You can use the HOME or Q keys to refocus on the protein.

- The density score of a residue may be viewed in the tab menu

spmm's picture
User offline. Last seen 11 weeks 1 day ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
scrolling in the tab popup to see the density score is no fun

for every single one of 95 segments - interesting concept.

jeff101's picture
User offline. Last seen 10 hours 42 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
Can you implement the Feedback ideas below?

http://fold.it/portal/node/1998645
Let "Segment Information" boxes brought up by tab be taller

http://fold.it/portal/node/997645
Use arrows to skim through the notes for each amino acid

Batz's picture
User offline. Last seen 2 weeks 4 days ago. Offline
Joined: 02/16/2012
Groups: Go Science
Problems with Cursor in selection mode

I mention this problem I already observed several times here, because it is really important for this puzzle:

If you want to move your stub (which is really necessary in this puzzle) with the cursor tool after pressing "3", and then you press "3" again to get rid of the cursor and your mouse is directly over the cross, Foldit crashes immediately...
this makes it even more impossible =/

Susume's picture
User offline. Last seen 9 hours 4 min ago. Offline
Joined: 10/02/2011
HINT

This ED cloud matches very well with stick view. The extra knobs on the backbone of the cloud line up with the extra twigs that show up between the sidechains in stick view.

Batz's picture
User offline. Last seen 2 weeks 4 days ago. Offline
Joined: 02/16/2012
Groups: Go Science
Another Hint

you can clearly see the aromatic residues like phenylalanine, tryptophan and tyrosine (there are two of them each), but also prolines that are good to begin with

However, you should be careful with mutating residues, for example the phenylalanines will be mutated to histidines because they are scoring better on the surface of the protein, although they will not fit exactly into the ED

jeff101's picture
User offline. Last seen 10 hours 42 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
Would hoops help?

I have mentioned this before, but Chat posts about this puzzle make it sound like hoops would be useful here. See the following for details:

http://fold.it/portal/node/992437#comment-19287
http://fold.it/portal/node/992670
http://fold.it/portal/node/989259

Joined: 09/24/2012
Groups: Go Science
is the segment ED score correct?

Is it normal that I find a segment completely out of the cloud with a density score of 90 ?

spmm's picture
User offline. Last seen 11 weeks 1 day ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
the cloud continues

my understanding is that the cloud and associated density score and pull on the protein, continues to repeat but is only visible in the central space so building 'outside of the visible cloud' can mess you up a bit - that could be incorrect of course, but now I just build inside the cloud and turn the view off and on frequently.

bkoep's picture
User offline. Last seen 9 hours 52 min ago. Offline
Joined: 11/15/2012
Groups: None
Correct

Most of these electron density maps are derived from protein crystals, in which a protein forms a regular lattice—you can imagine many copies of this protein aligning and arranging themselves into a 3D grid. We only visualize one "unit cell" of the crystal in the puzzle, but the density actually repeats itself infinitely in the X, Y, and Z directions.

Joined: 09/24/2012
Groups: Go Science
is it incorrect to have pieces of protein out of the unit cell?

Does the cloud that we see correspond to about une protein? (transborder puzzle would then be wrong)
Or is it possible that the protein we are trying to find "crosses" several unit cells?

spmm's picture
User offline. Last seen 11 weeks 1 day ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
This may help

I found this explanation with pictures helped me to understand the positioning but this is one example and unlikely to be the same for every cloud we get.

http://www.ruppweb.org/Xray/tutorial/bpti.htm

spmm's picture
User offline. Last seen 11 weeks 1 day ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
move tool is enormous

and completely blocks the view of the seg you are trying to manipulate when you are zoomed in

Batz's picture
User offline. Last seen 2 weeks 4 days ago. Offline
Joined: 02/16/2012
Groups: Go Science
https://fold.it/portal/node/1
spmm's picture
User offline. Last seen 11 weeks 1 day ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
sticks not balls as markers

would be much better as well, like the tools crystallographers use:

http://www-structmed.cimr.cam.ac.uk/Course/Fitting/fittingtalk.html

the 'dots' in foldit don't help to show direction along either the backbone or the 'arm' of a sidechain.

Joined: 09/24/2012
Groups: Go Science
interesting

Thanks spmm, it's interesting to see this course for crystallographers, using quite exactly what we try to do manually with electron density puzzles.

I like the conclusion: "Most people refine ad tedium, until they are bored."

Joined: 09/24/2012
Groups: Go Science
95 residues?

We do not succeed to go over 94 residues. Does anybody get 95 residues?

beta_helix's picture
User offline. Last seen 12 hours 7 min ago. Offline
Joined: 05/09/2008
Groups: None
Were you able to figure this out?

I noticed you top-scoring soloist solution had 95 residues.

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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