Assuming I already have a structure of a receptor bound to a peptide and I want to identify base pair substitutions in the peptide that can increase its affinity.
There are many criteria according to which a peptide could be modified in order to optimize its bonding to a receptor's site. Among them, just to mention some, are hydrophobicity, bulkiness, antigenicity, ... . However, I think the most promising one is the antisense-peptides strategy that offers the advantage of selectivity as an extra.
There were plenty of computer algorithms at 80-90s, when I was still active on these.
Hi Stephen,
if you have the crystal structure, Molecular Dynamics simulations might be one of the best options.
Best,
Ezequiel
If you have structure or decent homology model, I had good results with free FoldX or commercial MOE, to predict interaction stabilizing mutations.
http://foldxsuite.crg.eu
https://www.chemcomp.com/Products.htm
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