FlexPepDock: Difference between revisions
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==1. Create an input structure for FlexPepDock== | ==1. Create an input structure for FlexPepDock== | ||
You can generate peptide coordinates using Pymol (Build->Residue->Alanine). If you want an extended peptide, it is best to generate coordinates for poly-Ala first, and | You can generate peptide coordinates using Pymol (Build->Residue->Alanine). If you want an extended peptide, it is best to generate coordinates for poly-Ala first, and then mutate to your peptide using the mutation wizard (Wizard->Mutagenesis). <br> | ||
'''Important note:''' FlexPepDock does not change your Psi angles, so make sure that a proline is in trans if that's what you want!! | |||
Revision as of 00:43, 7 May 2013
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
You can generate peptide coordinates using Pymol (Build->Residue->Alanine). If you want an extended peptide, it is best to generate coordinates for poly-Ala first, and then mutate to your peptide using the mutation wizard (Wizard->Mutagenesis).
Important note: FlexPepDock does not change your Psi angles, so make sure that a proline is in trans if that's what you want!!