| 'Search ChEMBL Database' function [message #376] |
Mon, 27 August 2018 21:46  |
kerryfowler
Messages: 1
Registered: July 2014
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Junior Member |
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DataWarrior is the tool I've wanted for decades, so thanks to all the developers!
In version 4.7.2 the "Search ChEMBL Database..." function works for
similar structure to (sometimes)
equal structure to
stereo isomers of
tautomers of
but not for "superstructures of" which returns the message "Error in task 'Search ChEMBL Database': Your query did not retrieve any records."
The similarity search sometimes returns an error until the similarity threshold is lowered. For example, similarity search for dopamine as query fails until similarity is decreased from 90% to %89. Substructure query fails for dopamine.
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| Re: 'Search ChEMBL Database' function [message #1890 is a reply to message #378] |
Mon, 01 May 2023 16:45  |
rkp@23
Messages: 3
Registered: April 2023
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Junior Member |
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I am having a similar issue,
I am trying to query organohalides on ChemBL and searching using the "superstructures of" filter.
The search did not yield any result.
I have attached a screenshot of the query I used.
Is there any issue with the ChemBL server search in the version 5.5.0?
[Updated on: Mon, 01 May 2023 16:47] Report message to a moderator |
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| Re: 'Search ChEMBL Database' function [message #1905 is a reply to message #1890] |
Sat, 27 May 2023 18:01 |
thomas
Messages: 715
Registered: June 2014
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Senior Member |
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Assuming that your '[3]' atom list contains Cl,Br,I I could confirm that no rows are returned on the current chembl server with the version 32 database. It also shows a message that your search is not specific enough and would return too many records. If you use the same query, but use iodine instead of all three halogene atoms, then 101'394 rows are returned containing 10'531 distinct structures. Currently, the server limits results to 50'000 distinct structures for sub-structure queries and to 100'000 structures for other structure searches. The idea of the limit is a historic one to make sure that a result download is not taking forever and both, client and server resources are fit to handle the result. For the next server version I will increase these limits by a factor of 2.
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