Hi,
I have a protien peptide complex and I want to design a peptide that will bind to the protein better the the WT peptide. What tools do you suggest I use? it can also be from
any of the other rosseta platform (or any other). My goal is to find 50 potential peptides and then test them experimentally.
Thanks,
Miriam
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Post Situation:
I'd probably point you in the direction of the Furman Lab servers.
I don't know how well the design portion of things is "serverized", but if you're willing to use the command line version of Rosetta, you can get a start on the protocol by following the Meiler Lab tutorials, particularly, the "Protein Scaffold and Motif Design" one.
Thank you
From what I can see, peptide derive just finds the amino acids sequences that are in the protein already (devides it into segments), it dosn't find new peptides that will bind better (with differernt sequences)
Is this correct? If not, please explain how I can use it to find new sequences that bind in higher affinities.
Thank you
Yes, PeptiDerive just identifies "hotspot" peptides on existing interfaces. For actual design, you need a different algorithm. The Furman lab site I pointed to mentions some protocols (FlexPepDesign, FlexPepBind) which may be useful for this -- I don't know if there are online servers for them, though.
The Peptide design tutorial I tried to link to (but accidentally mistitled) doesn't actually do much mutation prediction, but the other tutorials on that page should get you started for using a local version of Rosetta. There's actually little difference between antibody-antigen design or thermostabilization (or small molecule interface design, for that matter) and peptide design. The same general approaches can be used, just with a protein-peptide interface. The one thing which you might consider, though, is to take your predicted designs and then redock them to see if the backbone conformation changes. You can actually attempt an interative approach, where you design to a fixed backbone, redock the new design with FlexPepDock, redesign to the new backbone, then repeat. Hopefully, you'll come up with designs which redock to the intended conformation and also don't mutate when run through the design process. Those should be good candidates to test.