My protein of interest has 3D structure available in pdb. I know about an snp that produces short isoform of that protein. How or using what tool I can produce that isoform as a pdb file?
You can use modeller to model the mutant protein by using PDB as template.
You can do it using Swiss PDB viewer, but if you are looking for a tool
this one is great for doing that, just upload your pdb file, write you snp in form of XPosY
and select the chain
http://bleoberis.bioc.cam.ac.uk/duet/stability
it will also calculate all the stability changes upon that mutation
Thanks.
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