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 ... ?