puzzle picture
263: Alignment Freestyle
Status: Closed


Name: 263: Alignment Freestyle
Status: Closed
Created: 02/23/2010
Points: 100
Expired: 02/26/2010 - 23:00
Difficulty: Intermediate
Description: This is the first sequence alignment puzzle! You can choose "Show Alignment" from the Actions tab to use the new sequence alignment tool. See if you can find a better alignment than the starting one for this structure!

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lilovip's picture
User offline. Last seen 1 year 20 weeks ago. Offline
Joined: 11/11/2009
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Alignment variants

Let's look what alignment variants we actually have at this puzzle. It's easy to see there is only one place where we can play with alignment sequence: at the place of 2-aa size space. Changing at any other places will cause huge alignment points reduce. Known protein has the following aa sequence at that place:
And our protein has at start:
So, now we can place two spaces within this six positions as we wish: they all will give 121 alignment points. I've tryed almost all of the variants. There is table of points for some of them (after alignment and the same sequence of recipes, which I found good):
xLSxPE 9026
LSPExx 9073
LSxxPE 9105
LxxSPE 9133
xxLSPE 9200
LxSPxE 9260
The last one is the best I think, so I've played with it some more time, and now I have 9293 points. If you can to proof any other alignment variant is better, post it here, please.
Happy folding.

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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, Boehringer Ingelheim, RosettaCommons