Docking and density

[John Kuszewski]

In article <3vlujd$j5p at netnews.upenn.edu>, "Jeffrey S. Taylor" <jeff at aries.wistar.upenn.edu> writes:

|> 	Does anyone know of a program to calculate density from atom
|> coordinates that will help me with this?  Any other ideas for checking

Easy.  Use xplor to get the number of atoms that are "near" (say, within
5 Angstroms) each atom.  The atoms at the interface should, by your
boss's reasoning, not be outliers.

|> the model's validity would be appreciated.  I should say that I built
|> the model with CHarMM, so the energetics are basically good, with 
|> attention payed to charge and hydrophobic complementarity.

How did you pay attention to hydrophobic complementarity?  Just by
eyeballing it, or did you do something quantitative?


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John Kuszewski                     ||  |/  /|  ||      
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