Hi All-
I've developed some models using MODELLER using mostly the "default" parameters shown in the tutorials. We wanted to look at the electrostatic surfaces of the proteins, but realized we were doing so without side-chain hydrogens.
I compared a two solved structures of the same protein, one from NMR and the other from x-ray crystallography -- and also stripped the NMR structure of its hydrogens. Then I used the program MOLMOL to look at the electrostatic surfaces -- resulting in a difference between models w/ and w/o hydrogens.
I've got a few questions about this:
1. I think I read on a previous discussion that you can add hydrogens to models during the modeling process -- how "exact" is MODELLER at placing the hydrogens? i.e. orientation of the hydrogens, pKa estimation of side-chains, etc ...
2. Is there any way to add the hydrogens after developing the model using MODELLER (or another program) -- that would not be difficult?
3. Is it normal convention to develop models with side-chain hydrogens -- or only in certain circumstances? I have not looked much yet, but I don't think that models developed and published in other papers are submitted to the protein databank ... ?
Thanks for your input, Doug Kojetin