We've been looking at the results from the first alignment puzzle, and they are definitely encouraging! In this case, we know the native (the protein structure we are trying to find). Here's an image with the template from the puzzle in red, the native in green, and the top scoring structure (produced by TheGUmmer and Madde) in blue. So the question is, can we get from threading the red template to the green native?

You can see that the main difference between the red and green structures is that loop on the left side. But the blue solution structure has gotten much closer to the native! The alignment that was used to make the solution was:

-MEYVEALYQFDPQQDGDLGLKPGDKVQLLEKL-SP-EWYKGSCNGRTGIFPANYVKPAF
AMATAVALYNFAGEQPGDLAFKKGDVITILKKSDSQNDWWTGRTNGKEGIFPANYVR-VS

For comparison, The starting alignment for the puzzle was:

-MEYVEALYQFDPQQDGDLGLKPGDKVQLLEKLSP--EWYKGSCNGRTGIFPANYVKPAF
AMATAVALYNFAGEQPGDLAFKKGDVITILKKSDSQNDWWTGRTNGKEGIFPANYVRVS-

So they're pretty similar, but sometimes small alignment changes can make a difference. Excellent work!

( Posted by  Seth Cooper 194 16669  |  Sun, 02/28/2010 - 22:29  |  0 comments )