8 Oct
2025
8 Oct
'25
5:43 a.m.
I’m dealing with two structurally similar proteins, one of which is in complex with a ligand (pdb1). The second protein is in the apo-form (pdb2). I’ve used matchmaker to superimpose the structures. Does it make sense to append the ligand coordinates to pdb2? I’m interested to find out which residues lie within 4-5 Å from the ligand. Probably a better approach would be to dock the ligand to pdb2. Could this be done through ChimeraX using Boltz2? Thank you for your suggestions. George