Retrieving Markush structure from compound collection

Hello,

I wonder if it is possible to automatically generate a covering Markush structure from a collection of compounds using the Java API.

I could think of a mechanism which combines MCS calculation with R-group decomposition.

Do you have any ideas or plans related to this issue?

Greets, Ingo

Hi Ingo,

Yes, it is possible if there is a common scaffold.
We are just adding a Markush output into R-group decomposition in version 5.3.
(A pre-release is already available here: http://www.chemaxon.com/devel/jchem/index.html )

Please check documentation and API in the above package, under the following paths:

jchem\doc\user\RGroupDecomposition.html

jchem/doc/guide/rgdecomp/index.html

jchem/doc/api/chemaxon/sss/search/MarkushGenerator.html

For the identification of a common scaffold, you could use libMCS:
http://www.chemaxon.com/product/jklustor.html

API is also available:

http://chemaxon.com/jchem/doc/api/chemaxon/clustering/LibraryMCS.html

 

Let us know if you have any more questions.

 

Best regards,

Szabolcs

Szabolcs wrote:

Yes, it is possible if there is a common scaffold. We are just adding a Markush output into R-group decomposition in version 5.3.

Sounds great to me! My main concern was how to generate the missing R1, R2, ... nodes for R-group decomposition, but this problem seems to be solved:

As of JChem 5.3, a query without R-atoms will be automatically modified in setQuery(chemaxon.struc.Molecule): R-atoms will be added in place of implicit hydrogens by addRGroups(chemaxon.struc.Molecule).

Can you give an estimation when 5.3 becomes available?

 

Greets, Ingo

We just built the alpha: http://www.chemaxon.com/devel/jchem/

Final release is expected still this year.

Szabolcs