puzzle picture
1834: Coronavirus Anti-inflammatory Design: Round 3
Status: Closed


176jawz101 70 80  13,0148
177versat82 70 864 Rechenkraft.net13,0147
178Kiwegapa 70 540  13,0147
179lwelite 70 1855  13,0147
180Sadaharu06.jp 70 1855  13,0147
181Vman 70 1855 Void Crushers13,0147
182perimundo 70 1855  13,0147
183Pikkachurin 70 567  13,0147
184harvardman 66 154 Anthropic Dreams13,0147
185dahast.de 70 196  13,0146
186Hum 70 1855  13,0146
187fpc 14 56 Marvin's bunch13,0146
188Altercomp 70 165 Go Science13,0146
189LELE1964 70 1855  13,0146
190heather-1 70 130  13,0146
191hpaege 70 1855  13,0146
192Arne Heessels 70 305  13,0146
193RockOn 70 1855 Go Science13,0145
194not_publius 70 1855  13,0145
195Bucsan 70 807  13,0145
196ミツバチハッティ 70 1855  13,0145
197foley2k2 70 1855  13,0145
198Grom 70 1855 Russian team13,0145
199kvasirthewise 70 864 Gargleblasters13,0145
200Barry1321 70 1855  13,0145

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bkoep's picture
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Residue Count (max +275)
Penalizes extra residues inserted beyond the starting 152, at a cost of 55 points per residue. Players may use up to 157 residues in total.

Core Existence (max +1000)
Ensures that at least 25 percent of residues are buried in the core of the monomer unit.

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.

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

HuubR's picture
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Local versus global optimum

Thank you, bkoep, for (again) explaining the objectives that can give us bonus points. And thank you, and all of your fellow scientist working on this project, for your outstanding work!

Starting the puzzle with quite a high score is an interesting concept. I assume the reason why the initial score is so high, is because this protein was designed and folded by a very renowned player (see the puzzle description). Now the challenge to all of us is to improve that score.

In the (few) puzzles I played this far it was often not difficult to get the score well above the starting value by using a few simple actions, like apply and idealize secondary structure, shake, wiggle, but now all of that has already been done. I hope this does not scare off too many players, because it seems to be very hard to "get off the mark".

Starting at this high score might be a good way to encourage players to try different concepts for the secondary structure. In fact, that is what I did initially. I have a habit (in puzzles as well as in real life) of not always going with the crowd. Although I acknowledge that teamwork can be very powerful, I sometimes feel that there are already enough pairs of eyes looking at something from the same viewpoint, and then I tend to try a different perspective. There was an interesting discussion in global chat yesterday about teamwork, and about working in a local optimum versus trying to find the global optimum. I think it was LociOilingIRC who raised that point.

Having said all that, can I ask you, bkoep, or one of the other scientists, a question?

I wonder whether the score that we get in this puzzle is a good indication of how well a certain protein will stick to the binding site. Correct me if I'm wrong, but isn't most of this score made up of how well the protein itself was built up and folded?

What I tried is the following. Starting from the initial design (reset the puzzle), I moved the protein away from the binding site, and then tried to find a new (local) optimum by shaking and wiggling. In my mind, the number of points that you lose this way (or in other words, the number of points gained by placing the protein at the binding site and re-optimizing it there) would be an indication of how "sticky" the protein is. Again, please correct me if I'm wrong. I am not a molecular biologist, just an electrical engineer who likes puzzles.

Could you give us an idea why the score (and bonus points) were set up the way they are? Thanks!

HuubR's picture
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The answer was already there...

Looks like you had already answered my question, long before I asked it, in your blog post Analysis of protein binder designs. Thanks! Lots of interesting stuff in there, way more than I could ask for.

This gives me enough incentive to stop focussing on the score and go my own way. Don't know whether it will get us anywhere, but the least I can do is try.

Now there's only one question left: if I would indeed find a "sticky" protein, but with a Foldit score that is lower than most other players', how can I make sure that this design is noticed by you, the scientists? Should I just save a solution and "Upload For Scientists" (in the Open/Share Solutions dialog box)?

bkoep's picture
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Upload for Scientists

Yes! That's exactly what the Upload for Scientists button is for. If you think your solution is promising, but it doesn't make the leaderboards, use Upload for Scientists and we'll be sure to take a look.

Great questions, glad you were able to find our previous blog post!

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LociOiling's picture
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that's the secondary structure...

Not sure if that was a question, but that's the secondary structure for each segment, using the codes:

  • L - loop
  • H - helix
  • E - sheet

The recipe print protein and several others use this format.

Actual science tools like JPred use a similar format, but with "-" instead of "L" to indicate loop.

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