DockingProtocol

[Anonymous]

Greetings:

I have been trying to perform protein-peptide docking with rosettascripts. For the global docking I was using the DockingInitialPerturbation mover and for the local DockingProtocol, of course before doing the docking I optimize sidechains with Prepack. I really have some doubts about this, first try to use the move DockingProtocol only to do global and local, despite this, in the output it is observed that the second protein hardly moves, it does not change position much despite the fact that has the options well set to perform both types of docking, so choose to use the global docking’s own flags or use DockingInitialPerturbation first. After that, I watched and the protein explored and disturbed around each other quite a bit and so I thought about using DockingProtocol only for local docking and refinement. The other thing that happens to me is that, after having executed DockingInitialPerturbation and DockingProtocol, many structures with the same energy and different rms come out, when I look in the viewer it turns out that they are in the same place with respect to the other, pymol reports rmsd=0 ; I have thought that the fact that they have the same energy and are in the same place is due to the fact that when DockingInitialPerturbation was executed previously, several structures were in a similar region and then DockingProtocol through small disturbances moved them to the same place, yes this is so, shouldn’t they have similar rms with respect to the input pdb? The other thing, some terms of the score file like interface_score and rms are specific to the execution of DockingProtocol? Is there any way to add those terms to the execution of other movers? I have looked at the weights of the functions used in DockingProtocol, but I don’t think they are actual energy terms, but rather additional information pertaining to the execution. I hope you can help me, thanks in advance.

[Anonymous]

Hi,

based on the first sentence of your post, you are trying to do peptide-protein docking but in the rest of the text, you refer to 2 larger proteins (I assume). Which one is more accurate? How long are the partners? If this is indeed a peptide-protein interaction, the global docking protocols PIPER-FlexPepDock and the recently published PatchMAN might be more beneficial, with a follow-up high-resolution refinement with FlexPepDock.

[Anonymous]

I understand, I am talking about the same complex throughout the publication. At first I tried to use FlexPepDock, but I always got an error in the attributes, especially in the score one, I don’t know why, the options and structure of the script were correct and I executed it several times, I’ll try to do it again, for this reason I opted for use the protein-protein docking procedure. About PatchMAN and PIPER-FlexPepDock, are they Movers or applications? Peptide has 12 residues and protein 750

[Anonymous]

Hi,

 

Can you please upload the flags and structures (XML if you are using RosettaScripts) that you are using for FlexPepDock?

PatchMAN and PIPER-FlexPepDock use Rosetta for local refinement but other softwares (PIPER and Master) for finding the docking site. You can try the PFPD server here: http://piperfpd.furmanlab.cs.huji.ac.il/ (PatchMAN’s will also be out soon, the github is here: https://github.com/Alisa-Kh/PatchMAN and also will be updated soon).

 

 

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