General advice on QSAR, toxicophore, integration

I am seeking general advice on using InstantJChem and/or other ChemAxon tools for calculating and identifying molecular properties including pharmacophores and/or toxicophores and using these properties in building QSAR models.

I am also interested in integration with data visualization and analysis. Currently, I use GraphPad Prism and JMP Pro for data visualization and analysis.

It is unclear to me which of the many JChem tools to use and how to integrate them. It would be ideal if there were a common interface, e.g., if the various JChem tools could be integrated into InstantJChem.

Finally, if anyone has experience using MOE or OpenEye software, I would be interested in how these tools compare with ChemAxon for such things as toxicophore or pharmacophore analysis and QSAR model building.

Thank you.

-- Rudy 

Dear Rudy,

 

Pharmacophore properties can be percieved by our pharmacophore
mapper utility. This is a 2D (topology based) approach, where the
desired pharmacophore types can be defined in an xml configuration
file. To find out more about this functionality, please visit

https://www.chemaxon.com/jchem/doc/user/PMapper.html />


There is a large collection of other descriptors that can be
accessed in our calculator plugins. These are available separately
and also in Instant JChem. You can find details on our
calculations if you visit this URL:  http://www.chemaxon.com/products/calculator-plugins/ />


Other molecular descriptors are described here: http://www.chemaxon.com/jchem/doc/user/GenerateMD.html />


I would also like to point your attention to our virtual screening
technology, Screen. Screen is basically a ligand based virtual
high throughput screening engine that can utilize topology based
(2D) similarity comparison, as well as 3D shape similarity
comparison of molecules. Details are here: http://www.chemaxon.com/products/screen/ />


Although we do not provide QSAR models, our calculated descriptors
including the above pharmacophore properties are widely used in
building such models. Currently the most integrated JChem based
application is indeed Instant JChem, that provides (as pointed out
above) access to a large collection of descriptors. This also
allows you to build simple QSAR models within the application. The
calculations for this can be accessed via Chemical Terms: http://www.chemaxon.com/marvin/help/chemicalterms/ChemicalTerms.html />
Nevertheless, JChem for Excel can also be applied for these tasks,
as it combines the chemical intelligence of the JChem platform
with the functionality of MS Excel. We are also working on an even
more integrated platform that can cover more in a single
application (including Screen for instance).



As on the toxicity: We do not have toxicophore and toxicity
prediction tools available at the moment, however, we have
developed some pilot tools which are potential candidates for
that. Building basic QSAR models, however, even for toxicity
prediction is possible with the help of the built in support for
the matching Chemical Terms functions in Instant JChem.

 

I hope this helps,

Ivan

isolt wrote:

Dear Ivan, Thank you again for your detailed response to my questions about ChemAxon products and their relationships to QSAR, cheminformatics, fingerprints, and pharmacophores or toxicophores. ChemAxon products are excellent and highly useful. I hope that they will continue to develop in such a way that ultimately an interface such as that for InstantJChem or perhaps Plexus could be used in like manner to the CCG MOE or BioClipse interfaces for doing QSAR models, chemical fingerprints, pharmacophores or toxicophores. Thank you. Best regards, Rudy Dear Rudy, Pharmacophore properties can be percieved by our pharmacophore mapper utility. This is a 2D (topology based) approach, where the desired pharmacophore types can be defined in an xml configuration file. To find out more about this functionality, please visit  https://www.chemaxon.com/jchem/doc/user/PMapper.html /> There is a large collection of other descriptors that can be accessed in our calculator plugins. These are available separately and also in Instant JChem. You can find details on our calculations if you visit this URL:  http://www.chemaxon.com/products/calculator-plugins/ /> Other molecular descriptors are described here: http://www.chemaxon.com/jchem/doc/user/GenerateMD.html /> I would also like to point your attention to our virtual screening technology, Screen. Screen is basically a ligand based virtual high throughput screening engine that can utilize topology based (2D) similarity comparison, as well as 3D shape similarity comparison of molecules. Details are here: http://www.chemaxon.com/products/screen/ /> Although we do not provide QSAR models, our calculated descriptors including the above pharmacophore properties are widely used in building such models. Currently the most integrated JChem based application is indeed Instant JChem, that provides (as pointed out above) access to a large collection of descriptors. This also allows you to build simple QSAR models within the application. The calculations for this can be accessed via Chemical Terms: http://www.chemaxon.com/marvin/help/chemicalterms/ChemicalTerms.html /> Nevertheless, JChem for Excel can also be applied for these tasks, as it combines the chemical intelligence of the JChem platform with the functionality of MS Excel. We are also working on an even more integrated platform that can cover more in a single application (including Screen for instance). As on the toxicity: We do not have toxicophore and toxicity prediction tools available at the moment, however, we have developed some pilot tools which are potential candidates for that. Building basic QSAR models, however, even for toxicity prediction is possible with the help of the built in support for the matching Chemical Terms functions in Instant JChem.   I hope this helps, Ivan