Hi, I’m investigating the binding mechanisms for proteins in relation to peptides as part of my research. The protein (the larger protein) isn’t directly from a pdb file, it has been altered so that only the region of interest is present as opposed to the entire sequence. Does anybody know where I would go about locating the active residues for this?
I am not sure I totally understood your question, do you have a PDB file with the part of the protein you want to dock? And do you have a similar PDB files for the peptide? If you have both and do not have experimental data to drive the docking with HADDOCK, you can use BioInformatics prediction. We provide a web portal called CPORT that can be used to predict active and passive residues preliminary to a HADDOCK run: https://milou.science.uu.nl/services/CPORT/
That’s a good start if you really have no data at hands to drive your docking run.
Thank you, that was what I needed