There are some reported sequences -derived from different proteins- that may have roles in specific function like cell attachment. Now I want to design a new peptide for example with amplified function. How do I begin? which software or bioinformatics tools should I use?
It depends if you have a target or not.
Most of the time, one would study the natural protein (for instance the cytokine binding to its receptor) to identify the putative binding site (if not known). Then you have to define the contribution of each amino acid to the binding zone, and determine which could be replaced / enriched.
This is part of the work I did in one of my previous work, just ask for more info if needed.
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Shouldn't you decide which target you're interested in first?. Anyway, just a few ideas:
I would recommend finding some interaction for which there is a PDB structure, at least you will have a solid starting point for your design.
Based on the structure, you will have more chance of success if you pick some fragment that is in an extended conformation in the complex. If you pick an alpha helix then you'll run into a whole lot of trouble related with folding and conformational stability of your peptide. Forget about beta sheets or hairpins, you'd have to deal with aggregation.
Before you start, you have be sure that you have a reliable source of recombinant protein in the mg scale for your tests, and a good assay available to test binding, otherwise you're wasting your time. I cannot stress this enough, you need protein to test your designs and if you can't have it, you are doomed.
Last, pick a few papers where they describe studies with model peptides as substitutes of protein-protein interactions. There are many details and alternatives along the way from design to having a functional peptide or probe!!
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