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How can I set up the protonation state of my histidine sidechains?
Up to table of contentsThis FAQ applies to: AutoDock 3, AutoDock 4
Histidines can be neutral or positively charged. When neutral, they can be protonated at the delta (HD1) or epsilon (HE2) positions. How can I set these up?
Using ADT
There is a command in ADT to help you decide on the protonation of the Histidines, but you have to load the commands before you can use it: go to "File > Load Module" and then scroll down, click on "repairCommands", and then click "Load Module" followed by "Dismiss". Now, go to "Edit > Hydrogens > Edit Histidine Hydrogens".
If there are any histidines in your molecule, a panel will open up listing each histidine residue along with a row of radio buttons. You can use these to choose whether each histidine should be neutral, HD1; neutral, HE2; or protonated.
Using Reduce/Molprobity
There is a very nice tool called Reduce (with a web-accessible front end called Molprobity) that can be used for adding hydrogens and optimising the hydrogen-bond network by flipping amido groups in Asn and Gln sidechains, and His imidazole rings by 180º. It can also be used for evaluating the quality of your protein structure. See:
Word, et al. (1999) "Asparagine and glutamine: using hydrogen atom contacts in the choice of sidechain amide orientation" J. Mol. Biol. 285, 1733-1745.