I would like to search a receptor patch recognized by a protein ligand. My jobs run into error of ligand patch can not be retrieved (the ligand is defined as one or a few amino acids). I wonder if patch search can perform such analysis rather than small molecule binding pocket.
Hello,
The patchSearch program can compare a ligand binding site on one or several protein surfaces. But, it is mandatory that in the PDB file, a ligand is present. It is detected with the character string “HETATM”.
In your PDB file, except for water molecules, there is only the protein and no ligand.
This explains the error.
If you want to compare the patch around residues of a protein, you must change, in the PDB file, at the beginning of each line "ATOM " by “HETATM” and, this, for each atom composing these residues of interest.
However, keep in mind that PatchSearch is not developed for this task.
Kind regards,
Gautier Moroy.