[Chimera-users] modeling non-standard amino acids

[Dan Wendt]

Hello,

My name is Daniel Wendt and I work for Biomarin Pharmaceuticals in Novato, Ca.  I'm trying to use Chimera's modeling software to predict structural changes that are imparted on my 22 amino acid peptide by the insertion of two non-standard changes to the peptide bond.  In one case, I am adding a methyl group to the backbone amide bond.  In another case, I'm removing a carbonyl from the backbone amide bond.  This peptide then needs to be cyclized by the formation of a intra-disulfide bond.  I do have x-ray crystal structure data of my cyclized peptide bound to one of its receptors.  Do you know how one goes about doing this?  Do you have any references that might help?

Thank you in advance!

Daniel Wendt

Senior Scientist
BioMarin Pharmaceutical
Novato, Ca 94949
(415) 506-6131
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