Hello Christoph,
Thank you for your message and for the hint on the reference literature. No
- until now I did not get an answer on my question but only the following
response:
Your mail to 'Cdk-user' with the subject
KNIME/CDK calculations: problems with logP and TPSA
Is being held until the list moderator can review it for approval.
The reason it is being held:
Post by non-member to a members-only list
Either the message will get posted to the list, or you will receive
notification of the moderator's decision.
I supposed that I would not get an answer without becoming a member of the
list or that there is an answer only at the internet pages.
Maybe I used the wrong Knime components for the calculation of the logP?
Here is the scheme used for the calculation:
SDF_Reader -> SDF_to_CDK -> XLogP -> XLS_Writer
I am still very interested in getting to know how to calculate XlogP data
with Knime. Thank you in advance for any help.
With best regards
Christian
Christoph
Steinbeck
<[EMAIL PROTECTED] An
.uk> Christian Grunwald
<[EMAIL PROTECTED]>
26.08.2008 16:46 Kopie
[email protected],
Thorsten Meinl
<[EMAIL PROTECTED]>,
Michael Berthold
<[EMAIL PROTECTED]>
Thema
Re: [Cdk-user] KNIME/CDK
calculations: problems with logP
and TPSA
Christian,
have you ever received any answer on this?
This message showed up in my mailbox only today (26-08-08) but seems to
have been sent 19 days ago.
CDK News issue 3/1 had an article on the logP quality assurance that we
did and shows how CDK logP performs vs. various other impls.
http://downloads.sourceforge.net/cdk/cdknews3.1.pdf
The values shown in these plots are certainly not in the range that you
report. The problem could have arisen from either the KNIME impl or some
changes introducing problems in CDK after the article was written
Cheers,
Chris
Christian Grunwald wrote:
> Dear colleagues,
>
> I was quite happy when I found out that it is possible to use KNIME for
> the calculation of ADME properties such as logP and TPSA. However, when I
> compared the results with reference data (PSA from Sybyl calculations,
logP
> from TSAR) there seems to be errors in CDK or KNIME or the CDK
> implementation in KNIME. Especially, logPs are calculated in a range from
> 15 to 45 but should be about 3. There are also sometimes differences of
> greater than 50 % between TPSA and Sybyl PSA data. What are the reasons
for
> this?
>
> Thank you very much in advance
> Christian
>
> ____________________________
> Dr. Christian Grunwald
> elbion GmbH
> Meissner Str. 191
> 01445 Radebeul
> Germany
> Phone: +49-351-4043 1552
> Fax: +49-351-4043 5552
> [EMAIL PROTECTED]
> www.elbion.com
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--
Dr. Christoph Steinbeck
Head of Chemoinformatics and Metabolism
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 2640
What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..
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