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 | ===========================================================================