SwissModel: It’s not what you think

One of the things that I’m always curious about, is the effect of a sequence variation on the conformation of a target.  Recently I wrote about ClinVar and SwissVar, two tools for examining variants and their associations with disease.  Since the PDB tends to have either wild type versions of a protein, or versions of the protein docked with some molecule, I thought it might be interesting to look at the mutant form of a protein.  Or at least what the predicted conformation of that protein might look like.

Expasy, the folks that brought you all SwissProt, have an interesting tool called SwissModel that lets you model a protein given a protein sequence.  I was curious about KRASG12D, so I pasted the edited sequence into SwissModel, and this was the result.

Image

Although, it’s not entirely visible from this screenshot, you can see the resulting models below.

KRASG12D - Model 1

KRASG12D – Model 1

KRASG12D - Model 2

KRASG12D – Model 2

KRASG12D - Model 3

KRASG12D – Model 3

 

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About aspenbio

I write software for scientists. I'm interested in Java/Groovy/Grails, the Semantic Web and Cancer Biology.
This entry was posted in Bioinformatics, Drug Development, Informatics, Science Blogging and tagged , , , . Bookmark the permalink.

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