Thanks, but as you say, it is not working. :-)
Another one out there?
Troels Emtekær Linnet
about 8 month again I used their dataset:
PINT: Protein-protein Interactions Thermodynamic Database.
Kumar MD, Gromiha MM.
Department of Biochemical Engineering and Science, Kyushu Institute of
Technology Iizuka 820-8502, Fukuoka, Japan. firstname.lastname@example.org
Unfortunately their website seems to be down right now, but maybe
dropping an email does the magic.
2011/8/24 Troels Emtekær Linnet <email@example.com>:
> ------------------------------------------------------------------------------> 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
> 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
> 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
> Then I will predict the pKa with propka and this script and compare.
> I am aware of:
> 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
> 04107 Leipzig, Tyskland
> Mobil: +49 1577-8944752
> EMC VNX: the world's simplest storage, starting under $10K
> The only unified storage solution that offers unified management
> Up to 160% more powerful than alternatives and 25% more efficient.
> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> PyMOL-users mailing list (PyMOLfirstname.lastname@example.org)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://email@example.com