Rosetta has been used to design inhibitory peptides. The design process will be much easier if you have a structure, not just sequence, of your target protein. The following articles may help.
Can Self-Inhibitory Peptides be Derived from the Interfaces of Globular Protein-Protein Interactions? by London et al.
Computationally designed peptide inhibitors against the Ubiquitin E3 Ligase SCFFbx4 by Lee et al.
Computational design of proteins targeting the conserved stem region of influenza hemagglutinin by Fleishman et al.
Computational design of the sequence and structure of a protein-binding peptide by Sammond et al.
Deanne Sammond: Thanks for the reply. However, Rosetta needs an estimated conformation for a peptide also. With our in vitro and in vivo data, we found that there is some specific amino acid whose phosphorylation can inhibit the activity of the protein. So, we are focussing to make some inhibitory peptide which can intearct with the amino acid and stop its phosphorylation, thus further its activity.
I never performed petide designing, however i had performed some molecular docking studies in the past. I will be thankful if u can provide me some idea as how to give some estimated conformation for a peptide.
Drawing inspiration from Nature is often a great starting point. Any structure showing your target protein bound to another protein at the site of phosphorylation can give you possible backbone conformations for a peptide inhibitor. Because Rosetta can build the peptide backbone from your input as to the desired secondary structure (helix/sheet/loop), you as the user can draw from or deviate from known structures as needed. Multiple design strategies can help you contend with issues of solubility or stabilizing the bound conformation.
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