Thanks, but as you say, it is not working. :-)
Another one out there?
Best
Troels
Troels Emtekær Linnet
Karl-Liebknecht-Straße 53, 2 RE <http://maps.google.dk/>
04107 Leipzig, Tyskland
Mobil: +49 1577-8944752
2011/8/24 Thomas Juettemann <juettem...@gmail.com>
> Hi Troels,
>
> 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. sh...@bse.kyutech.ac.jp
>
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347380/?tool=pubmed
>
> Unfortunately their website seems to be down right now, but maybe
> dropping an email does the magic.
>
> HTH,
> Thomas
>
> 2011/8/24 Troels Emtekær Linnet <tlin...@gmail.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
> > 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
> > 04107 Leipzig, Tyskland
> > Mobil: +49 1577-8944752
> >
> >
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