Hi, I am trying to dock a peptide sequence that I generated with that of a complex protein structure. I was using chimera and Autodock Vina to do the actual docking, and It's very difficult to define the parameters and it gives me error everytime I run the docking protocol. Can anyone help me out with the docking software for a peptide-protein docking and the procedures to do the actual docking? I am fairly new to this peptide-protein docking procedure. Thank you very much .I would really appreciate your help.
It is always best to start from scratch to learn by yourself. But to hasten the research you can use online server such as PatchDock, SwissDock, AutoDock, etc.
CABS-dock(biocomp.chem.uw.edu.pl/CABSdock): server for protein-peptide docking, server treats peptide backbone as fully flexible, while the flexibility of receptor proteins is limited to near-native backbone fluctuations.
FlexPepDock (flexpepdock.furmanlab.cs.huji.ac.il/) used for peptide-protein docking (refinement) protocol for the modeling of peptide-protein complexes, implemented in the Rosetta.
You can try Patchdock and then refine and rescore the Patchdock solutions with Firedock. Fire dock will give you results like the attachments. You can download the best 5 structures from Firedock and use the one with the lowest global energy of interaction just like Autodock.
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