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 Mark Fortner

I write software for scientists doing drug discovery and cancer research. I'm interested in Design Thinking, Agile Software Development, Web Components, Java, Javascript, Groovy, Grails, MongoDB, Firebase, microservices, the Semantic Web Drug Discovery and Cancer Biology.
This entry was posted in Bioinformatics, Drug Development, Informatics, Science Blogging and tagged , , , . Bookmark the permalink.

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