I have a scenario where I have a peptide-protein complex. I would like to thread a series of sequences over the peptide, then minimize the peptide-protein complex. The idea being, I would like to tell which threaded-peptide-sequences would be the "best" binder predictors. Or at least be able to segregate between potential non-binding sequences and binding sequences.
I've been looking at the backrub protocol. Would this be an appropriate application? I don't see immediately how I can thread the sequences over the peptide with this application then.
Then I've looked at the threading protocol. This looks like I can thread the series of sequences over the peptide, but I'd need fragment files for each new sequence? I don't exactly want this because I know the starting conformation of the peptide (even if I'm attempting to vary the sequence).
Then I've seen the fold and dock protocol. This looks decent because I know the starting conformation of the peptide when docked to the protein, but again, how can I thread a series of sequences over the peptide? And it a full fold-and-dock overkill?
Any advice would be greatly appreciated.
It sounds like you want flexpepdock (http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/d7/d...).
Generally if you have the _same_ length on all your peptides, you can do the "threading" trivially with fixbb, and then produce models any way you like: relax, backrub, flexpepdock...
If you have _different_ lengths, especially if you want indels, then the problem rapidly becomes much more complicated...I think the ab initio mode of flexpepdock is a good bet.
I would have the same length for all the threaded sequences (it's only a 7-mer peptide). So I guess this opens doors as far as which protocol to use for minimization?
I hadn't thought of FixBB (I don't know how I missed that), so I'll use that to thread the sequences. Then maybe backrub to minimize? Or would a full relax be better?
Sorry for the delay in reply...the forum system is being upgraded and forgot to keep sending me emails when others ask questions.
Backrub, relax, and refinement FlexPepDock are all options. I would use FlexPepDock because it is designed for the purpose, then relax as a second choice because I understand it better than backrub, and then backrub last. (Nothing wrong with backrub!) Frankly, this is a pretty empirical choice: all will work okay for the general purpose; try all three and see which gives the most consistent results!
How to thread a longer sequence on a smaller peptide? suppose I got peptide of length 7 and I want to thread sequence of length 13.
/\/\/\ to ---/\/\/\---, I mean I want to keep the middle portion threaded over available peptide BB conformation and give terminal residues extended conformation. I will use FlexPepDock in next stage to model the peptide.
I found a way to do this using PyRosetta but looking a alternative easier approach.
You may want to think about using the Remodel application:
It will be included in the next release of Rosetta, Rosetta 3.5, which should be released fairly soon.
I recently added this to the PyRosetta documentation if you havn't already seen it:
In my experience PyRosetta is probably about as easy as it gets for doing this. There is no generic "extension" module. I tried to write one and discovered that for everything but simple C-terminal extensions it's all corner cases.