Subject: CCL:Summary of pka database for carboxylic acids

From: "Donald Keidel" <dopetec-.at.-dslextreme.com>
Date: Tue, 22 Jul 2003 14:31:00 -0700

Last message I sent I did not include the summary...duh.  I want to
thank everyone for their responses and suggestions.  I ended
up using ACD Labs prediction software and I am currently developing a
binding affinity prediction equation with this information and other
data.  Sorry that the summary took so long to post, but I noticed today
that I never did it and had all the e-mails marked as unread.  Thank you
again.

Don

SUMMARY:

Hi Donald, 
if this is the case (you want to develop a computational prediction for
your database) I suggest you then to use our software MIPSIM to preform
a correlation between pka and molecular interaction potentials. It is
free for download for academics and the opnly think you need is to have
GAMESS (also free for academics) in your computer. 
You can also use GRID as your functuioin evaluator within MIPSIM, and I
think it is also free for academics. 
Currently we are working to make the output compatible with GOLPE in
order to get 3D-QSAR models from the dataset. I will tell Montserrat
Barbany, who is actually touching the code, to put a snapshot for you in
the web page when ready. 
The program can be found at 
<http://genome.imim.es/modeling/mipsim/> 
Please, let me know if you have troubles downloading it. 
I hope this cover your needs. 
Jordi 

Hello Don, Per your question, check-out Pharma Algorithms, ADME Boxes
software application www.admeboxes.com <http://www.admeboxes.com> The
evaluation software will give you 50 predictions for Ionization for
free. Sounds like an interesting project. I'd be interested to hear how
the software performed on your compound set. If you have further
questions, contact me at your convenience. Regards, Paulius Jurgutis
jurgutis-.at.-ap-algorithms.com <mailto:jurgutis-.at.-ap-algorithms.com>

Hi Donald,

Once I was looking for a pka database with Google and I found this file,
It may help you

Regards
Fabien

Dear Don,

     The NIST provides a fairly comprhensive database for <$500. 
Alternatively, you might look for a copy of "Critical Stability
Constants" by Martell and Smith in your local chemistry reading room.  

     good luck-

             Steve

Dear Mr. Keidel, 
Best database (not free) is shipped with ACDLab`s pKa estimation
software. 
Best wishes, 
Andras Borosy 

If it's only carboxylates, an empirical method will probably do ok.

If you don't want to splash out on a package, and only have 81
compounds, then you might like to try AcdLabs. It's not free but the
cost is reasonable on a per-compound basis via web interface, 
and their database seems pretty substantial. They can also 
give references in case a compound has been measured. 

Otherwise... there was recently a substantial thread about this on 
the Accelrys QSAR mailing list... if you can't find the archive online 
I can try to dig up some of the posts. qsar_society-.at.-accelrys.com

Hope this helps.

Jeremy

Hello Don,

I guess you have already looked for the NIST critical stability
constants? I found most of the logK-values I needed from there. In
addition to the deprotonation values it contains also complexation
constants with a variety of metal ions. Recently, the database has been
available also in the web. It very likely requires a license though.

Cheers,

Atte

------------------------------------------------------------------------
---------------------------------------
Donald J. Keidel
University of California, Riverside
Department of Biochemistry and Molecular Biology
Riverside, CA 92521
phone:  (909) 787-5493
fax:  (909) 787-4434
dopetec-.at.-dslextreme.com
webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm