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 > > ------------------------------------------------------------------------------ > 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 (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > ------------------------------------------------------------------------------ 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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
