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
Hi,
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.
Cheers,
Mensur
=========================================================================== | Mensur Dlakic, PhD | Tel: (734) 764-3554 | | Department of Biological Chemistry | Fax: (734) 615-3397 | | University of Michigan Medical School | http://www.umich.edu/~mensur/ | | 5416 Medical Science I | http://myprofile.cos.com/mensur | | Ann Arbor, MI 48109-0606 | E-mail: mensur@umich.edu | ===========================================================================
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Douglas Kojetin -
Mensur Dlakic