Subject: HTS Data Analysis Tools: Summary

From: David Clark <[email-masked]>
Date: Fri, 6 Dec 2002 08:30:40 -0000

Hi all

I promised a summary of responses to my query: "Does anyone have any
experience that they would be willing to share of tools for HTS data
analysis, particularly those that aim to help in the analysis of
(qualitative) SAR?".

Thanks to all who responded.

David Clark

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SUMMARY
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Dear David,

We used the ClassPharmer suite of programs (http://www.bioreason.com) for 
analysing HTS or virtual screening data.
It presents the advantage to cluster compounds by chemical scaffolds which 
are calculated on the fly. On the defined classes, you can perform various 
statistical analyses (e.g. scaffold enrichment, score distribution) for 
detecting false positives. The software can be downloaded from the 
Bioreason web site and used for a short evaluation.

Best regards
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Dr. Didier ROGNAN
Directeur de Recherches - CNRS
Laboratoire de Pharmacochimie de la Communication Cellulaire
UMR 7081
74, route du Rhin, B.P.24
F-67401 Illkirch

phone: +33 (0)3 90 24 42 35
fax: +33 (0)3 90 24 43 10
mobile: +33 (0)6 89 56 24 46
email: [email-masked]

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David! Take a look at http://www.leadid.de/project/index.html and
contact Marc directly for more info. Best, Christian

BioSolveIT GmbH, An der Ziegelei 75, 53757 St. Augustin, Germany
[email-masked], www.biosolveit.de, Tel/Fax: +49 2241 973 66 60/88

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Dear Dr. Clark,

may we draw your attention to the program SONNIA (formerly KMAP), which
could be applied to the analysis of data from high-throughput screening
by using neural networks?

The method of using neural networks for the classification and
prediction of biological activity and physicochemical properties (QSAR
and QSPR) was described in several publications, among these are:
* J. Sadowski, M. Wagener, J. Gasteiger, Assessing Similarity and
Diversity of Combinatorial Libraries by Spatial Autocorrelation
Functions and Neural Networks, Angew. Chem. Int. Ed. Engl., 34,
2674-2677 (1995)
* M. Wagener, J. Sadowski, J. Gasteiger, Autocorrelation of Molecular
Surface Properties for Modeling Corticosteroid Binding Globulin and
Cytosolic Ah Receptor Activity by Neural Networks, J. Am. Chem. Soc.,
117, 7769-7775 (1995)

The program SONNIA was developed to meet the needs of chemists, as it
provides many features for the visualization of chemical data.
For more information about this program please visit our websites at
http://212.168.36.43/software/sonnia/index.html .
We would be glad to provide you with an evaluation copy of SONNIA free
of charge for a test period of three months.

Hope this helps,

    Oliver Sacher

--
   Dr. Oliver Sacher
   Molecular Networks GmbH
   Nägelsbachstr. 25
   91052 Erlangen, Germany
   Tel.: +49-9131-815668
   Fax: +49-9131-815669
   Email: [email-masked]
   Web: http://www.mol-net.de

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Dear David,

May be the molecular modeling package of CCG called MOE might be of help.
It offers a nice binary QUASAR tool which is especially designed for HTSSAR
data.
May be you would like to check out the webpage: http://www.chemcomp.com/
There they have also publications for more details.
Also, they offer a 3 month evaluation period of their software.

Best regards,

Markus.
Markus Metz [[email-masked]]

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Dear David, 

Regarding your HTS SAR analysis tools question on CCL, [SARNavigator from
Tripos] fits ideally into this category. 
 
Best wishes, 

Andrew 

Dr Andrew W Sparkes - UK Sales Executive  (Tripos)
  
Tel: (01908) 650000 
Fax: (01908) 650001 
Andrew Sparkes [[email-masked]]

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Hi David,

Pharma Algorithms has developed the Algorithm Builder package
for building high-throughput screening algorithms using
SAR analyses based on recursive partitioning as well as fragmental methods.

I'll spare you the lengthy sales pitch and just point you to the link:
http://www.ap-algorithms.com/algorithm_builder.htm
and
http://www.ap-algorithms.com/qsar_builder.htm
Please note that Algorithm Builder contains all features of QSAR Builder.
QSAR builder has numerous tools for SAR, QSAR and QSPR analysis.

In most cases we will make evaluation copies available to interested users
for a 45-day period.
We make available a six-chapter tutorial that walks the user through the
software
using real data sets.

Also, the following page contains PDF files of scientific posters we have
presented in 2002
showing how SAR was used by our scientists in building algorithms for
Human Intestinal Permeation (qualitative filter) PGP substrate specificty
(qualitative)
and Acute Toxicity (qualitative and quantitative) among others:
http://www.ap-algorithms.com/presentations.htm

Let me know if you need any more information. I would be happy to oblige.

Very best regards,

Darius

Darius James Ross
European Marketing Manager
Pharma Algorithms
Tauro g-ve 12
Vilnius, LT-2001
Lithuania
eMail: [email-masked]
+370 5 262 34 08 (direct)
+370 5 262 37 28 (fax)
www.ap-algorithms.com
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Hi David, 
See: http://www.accelrys.com/cerius2/c2csar.html 

Kind regards,
Richard.
_________________________________________

Mr Richard Compton

Office Tel. +44 1223 228 500
Office Fax. +44 1223 228 501
Direct Tel. +44 1223 228 546
Mobile +44 7740 029 611

Web. http://www.accelrys.com 
Email. [email-masked]

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Dear David,

You may find useful the applications of Chemaxon, too:
http://www.chemaxon.com
Best regards,

Andras Borosy
Ph.D. computational chemist
Andras Borosy [[email-masked]]

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