New update: Protein Design!

We have posted an update with some exciting new features! This update contains tools for protein design, which will be accessible in some puzzles, and allow you to design completely new proteins! We should be posting some design competition puzzles soon, and in the meantime you can try out the new levels. There is more information about what's coming up in the blog.

Here are some of the new features:

Design: it is now possible to modify the sequence of proteins in some puzzles!

Band visualizations: you can now see the strength and length of bands.

Performance: Ctrl+Shft+L will render the protein with lines. Rendering stops if minimized on Windows, and should reduce CPU usage.

Levels: The levels have been adjusted, and there is a new interface for moving from one to the next. There are new levels for design.

Tools: We have cut down on the effectiveness of actions which don't change the backbone very much. This means that instead of chasing those last few decimals, you should explore larger changes to the protein. You will see this shift reflected in the change to the speed and effectiveness of all the tools.

(Thu, 05/21/2009 - 21:38  |  6 comments)
Brick's picture
User offline. Last seen 2 years 18 weeks ago. Offline
Joined: 07/15/2008
Groups: Beta Folders
Tool Changes?

Could you be more specific on what changes to the Tools have been made?

Joined: 11/20/2008
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.

quote: "Rendering stops if minimized on Windows, and should reduce CPU usage."

Works great, thanks for that!!!

Susanne's picture
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Joined: 11/09/2008
Groups: SETI.Germany
Design competition puzzles

I've never had so much fun, I've played them 3 times already, it's like being a kid in a sweet shop, can't decide which sidechain replacement to choose (no chemistry background here, so will be pure instinct and chance for me in that department). I am looking forward to using the new tools on a competition puzzle when it is released.
thanks to the dev team.

axcho's picture
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Joined: 12/18/2007
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Yes!

Finally, it's here! :D

Brick's picture
User offline. Last seen 2 years 18 weeks ago. Offline
Joined: 07/15/2008
Groups: Beta Folders
As usual, no guide

No guide on how to use the new tools effectively.

I finally found the new mode, but it seems as though the only option that works is to replace the sidechain with some other sort, and that doesn't seem to have very much (or any) effect. I suppose I could randomly try replacing each sidechain with one of the many alternatives, but that's just a grunt job, best left to a script or mechanized process. Is that available in the "cookbook" ?

There is a new function called "Mutate Sidechains", but it's not in the Design Mode area, and again it doesn't seem to do anything.

There are some right click tools in Design Mode that are labeled Insert and Cut, but they don't seem to work either, but since there is NO MANUAL on how to use them, perhaps I just haven't stumbled on the right combination. I would think if a section of backbone is highlighted, and Insert is chosen, that a new section is inserted. Evidently not. Similarly for the Cut operation - doesn't remove anything.

Sorry to rain on the parade, but Design Mode seems to be a bust.

Vman's picture
User offline. Last seen 1 year 28 weeks ago. Offline
Joined: 05/01/2009
Groups: Void Crushers
Not so bad

If you try the introduction puzzles the new tools becomce more clear. You should go back to intro and learn about them. Many times the insert and cut options do not do anthing because the circumstances are not right like for tweak.

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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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