Hi, I was thinking is it possible I generate a linear structure with AMBER and then use it in Abinitio module for de novo folding or I can generate a linear structure in Rosetta and use it.? Because from what I see, Abinitio only needs the fasta format and an input structure. So if my input structure is from PDB, then it doesn't make any sense to do de novo folding. In addition, how can I generate a fasta file with a certain protein seq i have in mind.? Thanks.
By the way, I also realised that Robetta is unable to generate fragments for protein sequences with less than 20 residues, so how can I generate fragments for a nonapeptide if I want to fold it.?
To your first question: ab initio does not require an input structure. It can take an input for RMSD benchmarking (where the correct answer is known, and you are testing if Rosetta gets it right). It only needs the fasta file.
To your second question: A nonapeptide is unlikely to have a rigid structure in solution, so folding it ab initio doesn't make sense, and folding it with fragments drawn from _folded_ proteins is inappropriate. Why do you want a free nonapeptide "structure"?
Oh, because I'm attempting to dock a nonapeptide onto a protein receptor, and I used the linear structure of the nonapeptide and it just seems to stay linear which is definitely inaccurate. Therefore, I'm thinking of folding the nonapeptide a bit, before I dock it onto the protein.
Were you using regular docking or the flexpepdock app? Flexpepdock does flexible peptide docking.
I was using the flexpepdock module.
Is it staying linear, or rigid? If it's rigid, there's a problem. If it's linear, that's probably what Rosetta thinks is best. I've brought this to the attention of the flexpepdock folks.
It stays rigid for the majority of the nonapeptide, while a small portion bent. Because I have done an MD simulation on this protein-peptide complex, so that's why I know that Rosetta didnt give me the results I wanted. Of course, it could be due to my flags. But I was thinking, even if Im using the basic flags, I would expect the linear structure of the peptide to change.
Could you provide the cmd-line you used? (Just to assess if the problem is not there...)
By the way, flexpepdock has an intrinsic option to let you start the simulation from an extended peptide ("-extend_peptide true" : start the protocol with the peptide in extended conformation (neglect original peptide conformation ; extend from the anchor residue)
Okie, my cmd-line is FlexPepDocking.linuxgccrelease @flags.basic > dock.log &. Anyway, I just read the manual again and I realise that the starting structure is to be an approximate of the final complex structure that I'm expecting. If that's the case, then it defeats my purpose in docking a linear peptide to the protein and hoping to see what and where would my final conformation of my peptide be like. So is it true that way or did I misinterpret anything.? Btw, I have added the extend_peptide flag but it seems to have no changes in the results at all.
You should remove the -flexpep_prepack flag, this flag should be used once to create 'prepacked' structure and then for the production run you should not use it.
Regarding your question, if you believe the peptide is 'close to linear' in its native conformation, FlexPepDock should still serve your needs, however, it wouldn't fold it into a helix or a beta hair-pin. If this is the level of sampling you're looking for, the next rosetta release will include the FlexPepDock ab-initio protocol that would have a much larger sampling range.
Okie, if let's say I have the native structure, but I wish to only change 1 or 2 residues, do you think it might still give me a relatively accurate result.? since I presume that there shouldn't be major changes to the secondary structure of the peptide.