Hey all, I've two questions, which I didn't found relevant post in the forum.
1. One of my protein has selenocysteine residues in it. How can I deal with it? I don't want to simply remove it since it's near to the active site. I assume I can just replace the atom name "SE" in the pdb with "S" and change "HETATM" to "ATM", but Se and S aren't the same size, which may cause different bond length?
2. One of my enzyme doesn't have substrate(galactose) molecule in its crystal structure, and I want to redesign it to bind to another substrate(glucose). Can I just first dock the original substrate into the enzyme and then put the new substrate into the same pocket and do a design?