Greg:
Thanks for the Info about Technical Database. The copy of MicroQSAR that we
have has SMILES input.
John
-----Original Message-----
From: DURST_GREGORY(_)LILLY.COM
To: qsar_society- -accelrys.com
Sent: 21/02/03 18:56
Subject: RE: QSAR - Looking for a pKa Prediction Program
We bought 'MicroQSAR' a long time ago, (about 1990?). I no longer work
at the same place, so I don't know if it still runs or is still in use,
(originally ran under Windows 3.1) It's supposedly still available
from:
Technical Database Ltd. Phone:(212) 245-0044 Fax: (212) 247-0587 email:
numerica#,#tds-tds.com
http://www.tds-tds.com/ind_num2.htm
It calculates a lot more properties than just pKa. Structure entry was
our main issue. It had it's own structure editor and couldn't read any
other fomat, so you had to draw in everything you wanted to calculate.
regards,
Greg
----------------
Greg Durst
Computational chemistry
Eli Lilly & Co.
Indianapolis, IN USA
Mark Earll <mark.earll]_[umetrics.co.uk>
Sent by: qsar_society-admin:_:accelrys.com
02/21/2003 06:52 AM
Please respond to qsar_society
To: "'qsar_society~~accelrys.com'"
<qsar_society.:.accelrys.com>
cc: "Karl Box (E-mail)" <karl.box]^[sirius-analytical.com>,
"Steve Elliot (E-mail)" <steve.elliot . sirius-analytical.com>
Subject: RE: QSAR - Looking for a pKa Prediction Program
Yvonne, John and Bob,
From my time in the lab measuring pKa's, I have always found that a 'by
analogy' estimation of pKa using the Perrin pKa books the best approach!
It is a great pity these books are out of print. I was not aware of the
MicroQSAR program, I would be interested to hear more.
I have used a few of the other programs in the past and they can work
well for single pKa values. Predictions for Multiprotic molecules are
often hopeless. An approach that can work well is to gather some
analogous molecules with known pKa's, put them through one of the
cheaper molecular property calculation packages and then build a PLS
model on the output. Unknowns with similar structures can then be
predicted quite well. This works quite nicely due to the model being
built over a small area of chemical property space but more ambitious
universal models can be problematic.
Is anyone working on reliably predicting multi-protic pKa's? I think
this must be a tricky hierarchical problem as the new electronic
structure of the protonated (or deprotonated) form must be taken into
account for the second or subsequent pKa. The problem gets worse with
zwitterions, especially flexible ones with internal H-bonding potential!
(then its time to dust off that electrode and head back to the lab....)
Mark
-- ------------------------------------------------------------------------ ----------- Mark Earll CChem MRSC Umetrics Senior Consultant (Scientific Data Analysis) Umetrics UK Ltd Woodside House, Woodside Road, Winkfield, Windsor, SL4 2DX Phone: 01344 885615 Mobile: 07765 402673 Email: mark.earll###umetrics.co.uk Fax: 01344 885410 Web: <http://www.umetrics.com/> http://www.umetrics.com ------------------------------------------------------------------------ -------------- -----Original Message----- From: Lipnick.Robert%x%epamail.epa.gov [mailto:Lipnick.Robert(0)epamail.epa.gov] Sent: 19 February 2003 19:15 To: qsar_society++accelrys.com Cc: 'qsar_society!A!accelrys.com'; qsar_society-admin!A!accelrys.com Subject: RE: QSAR - Looking for a pKa Prediction Program John and Yvonne, We are just recovering from a major snowstorm, so if there are more recent messages that make this obsolete, please ignore it. The program that Bob Hunter wrote, if I am correct, was based upon the Perrin pKa book that I found extremely useful for doing these calculations by hand. I made this know to Gil Veith and others at the EPA lab in Duluth, MN at the time, and I think they found funds for Bob Hunter to wrote the program. I don't have a copy myself, but would be interested in getting one, if it runs on a a PC. Bob =================================== Robert L. Lipnick, Ph.D. U.S. Environmental Protection Agency Office of Pollution Prevention and Toxics (7403M) ICC Building 1200 Pennsylvania Ave., N.W. Washington, DC 20460 TEL 202-564-7632 FAX 202-564-7450 lipnick.robert() epa.gov For FEDEX, etc. or visits: Dr. Robert L. Lipnick U.S. Environmental Protection Agency ICC Building 1201 Constitution Ave., N.W. Room 6308 LL Mail Stop 7403M Washington, DC 20460 ================================= Dearden John <J.C.Dearden],[livjm.ac.uk> Sent by: qsar_society-admin * accelrys.com 02/14/03 04:28 AM Please respond to qsar_society To: "'qsar_society ~~ accelrys.com'" <qsar_society##accelrys.com> cc: Subject: RE: QSAR - Looking for a pKa Prediction Program Yvonne: The pKa software packages that I'm aware of are: 1. Pallas from Compudrug ( <http://www.compudrug.com/> www.compudrug.com) 2. ChemSilico ( <http://www.chemsilico.com/> www.chemsilico.com) 3. SPARC ( <http://ibmlc2.chem.uga.edu/sparc> http://ibmlc2.chem.uga.edu/sparc) 4. ACD ( <http://www.acdlabs.com/> www.acdlabs.com) 5. MicroQSAR, which was written quite a few years ago by Bob Hunter. So far as I know, it isn't marketed any more. We have a copy, and Bob might be willing to allow others to use it. There may well be others that I haven't come across. John Dearden -----Original Message----- From: yvonne.c.martin]=[abbott.com [mailto:yvonne.c.martin _ abbott.com] Sent: 13 February 2003 17:33 To: qsar_society{}accelrys.com Subject: QSAR - Looking for a pKa Prediction Program Hi all, I am looking for a pKa prediction program that I can put on an internal web page. We would take care of getting the structure in the correct form and displaying the results. Obviously, the program must be reliable across many structural types, be deployable in the method described above, and be affordable. Replies from vendors are welcome, but please include approximate prices and how one can test out the program. Is there a limit on the number of structures processed? A time limit? Yvonne Martin Abbott LaboratoriesReceived on 2003-02-23 - 16:58 GMT
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