puzzle picture
428: H2N2 Flu Design Puzzle 2
Status: Closed


Name: 428: H2N2 Flu Design Puzzle 2
Status: Closed
Created: 06/07/2011
Points: 150
Expired: 06/13/2011 - 20:00
Difficulty: Intermediate
Description: The results from the first Flu puzzle were very interesting and we would like to give you a different subtype of the H2N2 Japan 1956 Influenza virus. The goal is to design the interface of these designs so that it can bind to the H2 subtype of Influenza. This puzzle is also worth 150 global points! If you are new to Foldit, make sure you have completed the Intro Puzzle 4-5 and Design Puzzles 6-1 through 6-4 and read the blog for more info about these Flu puzzles: fold.it/portal/blog
Categories: Design, Overall

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Joined: 12/06/2010
Groups: foldeRNA
i find that this sort of

i find that this sort of puzzle as the 425 are not easy to see because all is grey. Even if i change the view, it isn't easy to see the segments to mutate. It is because you want that to be more difficult or because it is the best way to show this puzzle? If not, and if some others people are agree with me, isn't possible to let the segments to change in green as the other's ones?

Sorry if my question is stupid.....

spmm's picture
User offline. Last seen 18 weeks 2 days ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
stating the obvious

Scripts were kindly provided by FoldeRNA and AD to set the aa sequence. There was apparently a difference of 12 segments between the two scripts, which may be of interest.
Neither script provided majic results unless presumably your position matched one of theirs.
Out of curiosity I ran some basic tests.

Test one - from a reset puzzle state, no other changes; I ran each script:
FoldeRNA AD Foldit mutate button at CI =1
12982 12393 13036

From a res√ęt puzzle after Blue Fuze for stabilisation I ran the scripts (using the same saved solution after fuze), then ravs repeat fuzes and 8 loops of compressor

FoldeRNA AD Foldit mutate button at CI =1
12970 12709 13087

The AD sequence did seem to have more wriggle room.

So very unlike the previous puzzle where Marie's aa sequence added points, probably because the position was more restricted.

So it is all about the position in this one although the position was still very restrained.
Of course the method may be incorrect however I restrained myself to using public scripts without any manual movements, so perhaps a different starting stabiliser and post mutate scripts may have made a big difference.

Joined: 06/17/2010

we need it 3rd time but w/o constrains this time? :)

gramps's picture
User offline. Last seen 7 years 34 weeks ago. Offline
Joined: 12/16/2010
Move Tool: they're not kidding about reviewing Tutorial 4-5 ...

Hat tips to AD team, especially tyggy and tyler for helping to clue me into the Move Tool (aka purple pointy compass rose) that makes games like this almost enjoyable.

Have a look at Tutorial Puzzle 4-5, "Moving Along" and its wiki hint (scroll down)

Having spent many hours banding, wiggling and praying these design ligands into position it was a blessed relief to realize you can move and rotate the whole ligand as follows:

with ligand in pull mode ...

... left-click on the backbone of the ligand to bring up the purple pointy Move Tool.

Now left-click and drag on the Move Tool to rotate the ligand in place.

Right-click and drag on the Move Tool will move the ligand around in the plane of the screen ...

... and, my favourite, shift-click and drag on the Move Tool to draw the ligand toward you or push it away.

deus911's picture
User offline. Last seen 1 day 54 min ago. Offline
Joined: 05/11/2008
Groups: foldeRNA
"Super antibody' fights off flu" - FI6


Wanted to mention it since it's related and interesting.

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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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