Re: [ccp4bb]: pKa value

[JP Cartailler <jp@bragg.bio.uci.edu>]

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Hi there,

I strongly recommend MEAD from Don Bashford's group at Scripps.  The setup
is tedious but the results are worth the investment in time.  The
theoritical pKa's it generated for one of our systems were very close to
the experimental values (within 0.1 pH unit) we had.

see: http://www.scripps.edu/bashford/

best,

JP

On Sat, 8 Mar 2003, cheom-gil cheong wrote:

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> 
> Dear all;
> 
> My protein has a tyrosine residue in the active site that is believed to act 
> as a catalytic acid. Since a lysine residue is close to it, we assume that 
> pKa value of the tyrosine is lower than that of the free amino acid. Does 
> anyone know a program that can theoretically calculate pKa value of a 
> specific residue from the coordinate of the protein?
> Many thanks in advance.
> 
> Sincerely,
> 
> Cheom-Gil Cheong, Ph.D.
> Research Associate
> Department of Molecular Biology
> The Scripps Research Institute
> cheomgilcheong@hotmail.com
> cheong@scripps.edu
> 
> 
> 
> 
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