Overlap Analysis

Hi,

I have been trying to do an overlap analysis of Compounds (TestCompounds.sdf) with Markush Strutcures (Patent_V1.mrv & Patent_V2.mrv). However, I couldn't find any HITS using the Compounds as input and Markush as target. Search mode is FULL with other associated parameters (SearchOptions.jpg).

I was able to reproduce the HITS for a smaller different set of Markush Structure and Compounds.

Thanks in advance.

Best Regards,
Anil

Hi Anil,

It has to do something with your Markush structures. I briefly checked them and found large number of so called pseudoatoms. These are groups like Halogen, Alkyl, Carboaryl, etc...

I'm sorry but we can't search among structures with those or by those groups. IJC is simple not able to translate those pseudo-atoms to normal chemical representation.

I recommend to draw structures using real atoms, without these 'label' atoms.

We will try to see if we are able to support pseudo atom queries in future.

Thanks,

Filip

Hi Filip,

The attached Markush file (Patent_W1.mrv) too has pseudoatoms. When i execute the Overlap Analysis using the Compounds(TestCompounds_W1.sdf) against this markush file, I get HITS.

Even for the earlier Markush file, i get HITS when i use the option Full Fragment. However, this process gives me FALSE positives.

Thanks for your time and support.

Best Regards,

Anil

Hi,

Any update????

Thanks,

Anil

Hi,

I'm sorry for the delay. This is peculiar issue. It seems as an issue with search types and their expectations. I don't fully understand the difference between full and full-fragment search. I will forward this to more competent colleagues.

You may also want to check the documentation at:

http://www.chemaxon.com/jchem/doc/user/query_searchtypes.html

Regards
Filip 

Hi Anil,

 

Could you tell me, please, what version of IJC are you using?

I have hits for the first compound in TestCompounds.sdf and Patent_V1.mrv and Patent_V2.mrv too.

 

Thank you,

Norbert

Hi,

I am using Instant JChem 6.3, following are complete details.

Instant JChem Version: 6.3.0 (build: 201405151859-b26c9726cbef)

JChem Version: 6.3.0 (build date: 2014-05-13, version ID: 6.3.0-82)

JChem Table Version: 6300000

Marvin Version: 6.3.0 (build date: 2014-05-13)

Java: 1.7.0_25; Java HotSpot(TM) 64-Bit Server VM 23.25-b01

System: Windows 7 version 6.1 running on amd64; Cp1252; en_US (instantjchem)

I have tested once more before replying to the post and i couldn't find any HITS.

Thanks for your time and support.

Best Regards,

Anil

Hi Anil,

 

Thank you for the details.

I've managed to reproduce the problem, so I have created an error-ticket for it. Not sure when we can fix it, but it is registered and will taken care of.

 

Best regards,

Norbert

Hi Norbert,

Thanks for the update.

Can I have the Ticket number or something to follow-up. If its not needed then I would follow-up with this post.

Thanks for your time and support.

Best Regards,

Anil

Hi Anil,

Sure, the internal ID is "JCB-732"; but there is no real need for it since we will follow up on the issue in this forum topic. 

Best regards,

Norbert

Hi Anil,

we have tested it in IJC version 14.7.21 and we think that the bug is fixed.

Thanks again for reporting this.

Filip

Hi Filip,

Thanks for the update.

I downloaded new version and verified the same. I confirm that the fix has been done.

Thanks for your time and support.

Regards,

Anil

Hi Anil,

I am glad to hear that. Thanks for your message!

Cheers,

Filip