I need to create peptides to use them as flexible ligands in docking (DockThor platform). I'm new at pyRosetta so I've only seen 1 tutorial until now. I'm using the following code
import pyrosetta
from pyrosetta import *
from pyrosetta.toolbox import *
init()
peptide_sequence = 'insert peptide sequence'
pose = pose_from_sequence(peptide_sequence)
scorefxn = get_fa_scorefxn()
# define variavel score before relax
score_before_relax = scorefxn(pose)
# Relaxa a pose
relax = pyrosetta.rosetta.protocols.relax.FastRelax()
relax.set_scorefxn(scorefxn)
relax.apply(pose)
# Calcula e imprime o score após o relaxation
score_after_relax = scorefxn(pose)
print('Sscore pre relax:', score_before_relax)
print('Score pos relax:', score_after_relax)
pose.dump_pdb('relaxedpeptide.pdb')
I don't know why but I can't insert them in DockThor platform, it shows an error when I try. When I open the .pdb pose in a text editor, there's no CONECT section as other .pdb files from cristalized peptides, I think maybe that can be the reason.
Is there some protocol to create small peptides (9~13 residues) for use in docking?
thanks
If someone can recommend a tutorial about ab initio peptide design in english, portuguese or spanish, it would be good too :)
Generally speaking, PDBs containing only canonical amino acids don't contain CONECT records. (The connections are implicit from the residue identities.) Rosetta takes that further, and (typically) does not read or write CONECT records, relying on residue parameter files (either from the database or provided by the user) to define the connectivity.
I'm not familiar with DockThor (it does not appear to be Rosetta-related) , but if it's a small molecule docking program then it may not be set up to take multi-residue peptides as input. You should probably read the help information and the references for DockThor to see what the format and requirements are for the docking peptide structures.
If you wanted to use a Rosetta program to do the docking, I would recommend the FlexPepDock protocol. There's a webserver at http://flexpepdock.furmanlab.cs.huji.ac.il/ or the Meiler Lab protein design workshop (https://meilerlab.org/rosetta-protein-design-workshop-2018/) has a Peptide Design tutorial which uses FlexPepDock. (You can adjust it to "design" to a single sequence.)