Hi pymolers.
I simple don't know where else so post this question. So I hope that some of
you guys can help me.
*I need a Database with protein experimental pKa values, with possibility to
search for Cysteines and .pdb structure*
Because, I have made a pymol script that predicts the pKa value for a
cysteine very precise.
The model is described in:
"Predicting Reactivities of Protein Surface Cysteines as Part of a Strategy
for Selective Multiple Labeling"
Maik H. Jacob, Dan Amir, Vladimir Ratner, Eugene Gussakowsky, and Elisha
Haas*
Biochemistry 2005, 44, 13664-13672
With help from Maik, we got it to work very good. I got a pearson
correlation coefficient of 0.90
and have batched up against propka, which gets 0.70
So, it looks like this script can be superior, at least for cysteine
predictions.
But to make the method more reliable, I need to find a database where
experimental pKa values for cysteines is reported, and a related .pdb
structure.
Then I will predict the pKa with propka and this script and compare.
I am aware of:*
http://www.ddg-pharmfac.net/ppd/PPD/pKasearch.htm*
But I could need a larger database.
If any have read some articles with cysteine pKa values, I would be happy to
hear about it.
Troels Emtekær Linnet
Karl-Liebknecht-Straße 53, 2 RE <http://maps.google.dk/>
04107 Leipzig, Tyskland
Mobil: +49 1577-8944752
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