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Re: surface electrostatics and hydrogens


See below for several quick answers.

On Thu, 3 Oct 2002, Douglas Kojetin wrote:

|>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 ...

If ProsaII and Procheck are to be believed, Modeller makes worse models
with hydrogens than without even when exactly the same alignments and
parameters are used. I have tried this only 2-3 times, so maybe my
experience is not representative. If true on a larger sample, I'm not sure
why this would be unless MODELLER's libraries with hydrogens are not
optimal. Any explanation from pros?

|>2.  Is there any way to add the hydrogens after developing the model
|>using MODELLER (or another program) -- that would not be difficult?

Adding hydrogens can be done easily using a very good (and fast) program
called Reduce that can be found at David & Jane Richardson's Web page
(http://kinemage.biochem.duke.edu). This program will also optimize Asn and
Gln sidechain amides, and His rings.



| Mensur Dlakic, PhD                    | Tel: (734) 764-3554             |
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