Generating Active Sites for Developed Protein

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:

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