How to add missing residues using swissPDBviewer

Question

[ranjuks641]

Hi,

I would like to perform docking with Autodock4.2.6. Before docking I would like to optimise the crystallized PDB structure by adding missing residues. How do I add missing residues by swissPDBviewer? I have 2 missing residues in the N terminal and one missing residue in the C terminal. How do I know the protonation state of Histidine residues? Is histidine should be protonated before docking?

Answer 1

[Mensur Dlakic]

SwissPDB viewer is not appropriate for this purpose. Most likely you don't need to add the missing residues, unless you have a reason to believe that your ligand binds near either of the two termini.

Hydrogens must be added to all protein residues before docking, and ligands need to be processed as well. You may want to consult a tutorial that covers all the steps.

http://autodock.scripps.edu/faqs-help/tutorial