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.


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