FlexPepDock

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FlexPepDock: Wanna dock a peptide? Use FlexPepDock!

Interested in peptide docking? Use FlexPepDock, which is a peptide docking software implemented in Rosetta. The easiest way to do that is to use the online server:
http://flexpepdock.furmanlab.cs.huji.ac.il


If you want to run FlexPepDock locally, follow the steps below.
In my example I docked the hexapeptide NT(8-13) with the sequence RRPYIL into the neurotensin receptor. I did this prospectively, without having looked at the bound peptide conformation before doing this. All I knew was that the C-terminal carboxylate interacts with Arg327 (Barroso et al, JBC, 2000) and that the peptide adopts an extended conformation (Luca et al, PNAS, 2003).

1. Create an input structure for FlexPepDock