Predicting pKas from PDBs

Wayne R. Baker baker at
Wed May 3 21:09:38 EST 1995

In bionet.molbio.proteins,  John Kuszewski <johnk at> wrote
:Does anyone know if there's a method to predict 
:the pKas of ionizable protein groups from 
:atomic coordinates?  

Quite a few, actually, although the accuracy is another matter. 

I believe DelPhi from Honig's group can do the calculations, which is
available for a small fee via anon ftp and also is in the package Insight.
Bashford et al [(1993) Biochemistry vol 32 p8055] has a program called
MEAD that is available for free via anon ftp. The reference has the info on
how to get it. I'm hoping to install it Real Soon so I can see how well
it does. Those are the only packages I know of that are available
for outside users.

Warshel has a program called POLARIS [Warshel et al (1984) PNAS vol 81
p4785] and there is an FDPB method described by Antosiewicz [(1994) vol 238
p415] that did a fairly good job on RNase A. And the ubiquitous Fred
Richards did this ages ago [Matthews & Richards (1982) Biochemistry vol.
21 p4989]. I don't know if any of these folks have made their packages
available for academic use; if you find out, lemme know. :-)

Wayne Baker (baker at		Maybe a great magnet pulls
Biochemistry & Biophysics		All souls towards truth
Iowa State University			-- k. d. lang, "Constant Craving"

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