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ChEMBL-DB Extractor

LigandScout Extensions for the KNIME Workbench version 1.7.9 by InteLigand GmbH

The ChEMBL-DB Extractor node fetches molecules from the ChEMBL database that show activity towards selected targets.


Query Settings

Textfield used for dynamically filtering the target table. Per-default, non case sensitive string comparison is done using all columns of the table. The *-literal can be used as a stand-in for an arbitrary string, '?' stands for any single character and '\' is needed to escape the '*' and '?' literals in case these should not be used as stand-ins but included in the actual search string.
Regular expression
Advanced users can use regular expressions for dynamically filtering the target table. The given expression will be interpreted by Oracle's Java implementation. For more details see https://docs.oracle.com/javase/7/docs/api/java/util/regex/Pattern.html
(Default: disabled)
Case sensitive
If selected, dynamic filtering of the target table will be done in a case sensitive manner. This affects both default filtering and regular expression filtering.
(Default: disabled)
Moves currently selected target entries to the selected targets list. The selected targets will be used to extract bioactivity assay compounds from the specified data source.
Adds the target currently specified by its ChEMBL ID in the textfield to the left to the selected targets list. Multiple ChEMBL IDs can be entered using any common separator (space, comma, etc.).
Remove selected
Removes targets from the selected targets list that are currently selected. Holding the ctrl button on the keyboard enables to select multiple entries at once.
Remove all
Removes all targets from the selected targets list.
Update Targets
Upon a click on this button, the specified data source will be used to retrieve all available targets and to update the table with this new data. This is only necessary if very recent ChEMBL data is needed. If the dialog is closed before the process is finished, the update will be cancelled.


Activity Filters
Only activities and subsequently compounds that comply with the filters set here will be retrieved. Therefore, these filters can shorten the node's execution time, especially when working with the public ChEMBL WEb Service API.
Filter Script
Valid JavaScript code placed here will be executed for each retrieved compound and must return true in order for the compound to be included in the results table.
tgtChEMBLID != ' < ChEMBLID to include > ' && cmpdMolWeight == < Floating point number for comparison >;
Available properties can be inserted via right click on the script editor area.

Data Source

If selected, the node will retrieve data from the URL of the ChEMBL-DB REST web-service specified. It should not be necessary to change the default URL.
(Default: enabled - https://www.ebi.ac.uk/chemblws/)
Relational ChEMBL-DB
If selected, the node will retrieve all data from a relational database server.
(Default: disabled)
ChEMBL Database Version
Version of the ChEMBL database to use. This is important because the schema changes from release to release. However, the node is generally able to determine the version on its own and the default setting should therefore be sufficient.
(Default: Auto)
DB-Driver to use, currently MySQL and PostgreSQL are supported.
(Default: com.mysql.cj.jdbc.Driver)
URL of the database server. Typically the following schema is used: <protocol>://<host>:<port><database_name>
Username of user that has permission to access the specified database on the database server.
Password for the specified user.

Output Ports

Table containing the molecules extracted from the ChEMBL database

Best Friends (Incoming)

Best Friends (Outgoing)


To use this node in KNIME, install LigandScout Extensions for the KNIME Workbench from the following update site:


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