Hello,I want to ask a question about protein-peptide docking. The peptide I used has about 30 residues, and it has no PDB structure, how can i upload the PDB? Thanks.
Hi,
it is difficult to upload a PDB if you don’t have one. Do you have any experimental information about the peptide? There are several tools describing how to build a peptide 3D structure from its sequence, one can also do it in Pymol. Check out this post: Peptide-protein tutorial
First,thank you very much,and you are so kind. Then I also want to ask you another question, the Peptide-protein tutorial introduces the Peptide-protein docking protocal using LINUX, I want to know whether we can use the online web server to do the docking, and whether i can do this using the Easy interface.Thanks
Sure, you can used the webserver once you have all PDBs needed for docking ready. You can also create an ensemble of peptide conformations with pdb_mkensemble in our new https://bianca.science.uu.nl/pdbtools/submit webserver. Peptide-protein docking is also described here: https://www.bonvinlab.org/education/molmod/docking/ . It would be useful to change the sampling parameters as described in the protocol and for this you will need the expert level access.
Thanks for your help, I have another question,I am so sorry that I cann’t find the pdb_maensemble in the first URL you givd me , and I can’t open the second URL. Then, because we don’t have a LINUX system，I want to know if there is a way to get a pdb of peptide but not use MD! This figure is the five stages of Protein-peptide docking introduced by the tutorial 无标题|690x324 .
It’s pdb_mkensemble
build your structure by using SWISS-Modeling or ITASSER, then upload your pdb.