REOS Tagger

This component flags input molecules according to the Rapid Elimination of Swill (REOS) filter rules, which are listed below.
The expected input is data in SMILES, SDF, Mol or RDKit molecule format.
In case a molecule violates one or more of the rules listed below, the according flags and abbreviations will be returned in a collection output column.
The component also allows checking for structural alerts as defined in various sources (see below). In case one or several structural alert rule sets are checked in the component's configuration window and a molecule contains such a structural alert, the first substructure from the list is highlighted in an additional output column. Note that the component only displays the first matching structural alert from the first selected rule set. Note that checking for structural alerts might take a while.
In case the input molecule matches neither a rule nor any structural alert, it will be flagged with "true" in the pass column.


MW: Molecular weight between 200 and 500
LogP: LogP between -5.0 and +5.0
HBD: H-bond donor count between 0 and 5
HBA: H-bond acceptor count between 0 and 10
FC: Formal charge between -2 and +2
RotB: Rotatable bond count between 0 and 8
HAC: Heavy atom count between 15 and 50

LINKS TO RULE SETS:
* Bristol-Myers Squibb HTS Deck Filters - europepmc.org/article/MED/16711725
* University of Dundee NTD Screening Library Filters - europepmc.org/article/MED/18064617
* Glaxo Wellcome Hard Filters - europepmc.org/article/MED/10529988
* Pfizer LINT filters - europepmc.org/article/MED/16787349
* NIH MLSMR Excluded Functionality Filters - yumpu.com/en/document/read/12367541/mlsmr-excluded-functionality-filters-nih-molecular-libraries-
* Pan Assay Interference Compounds (PAINS) Filters - europepmc.org/article/MED/20131845
* SureChEMBL - surechembl.org/knowledgebase/169485-non-medchem-friendly-smarts

OTHER INTERESTING LINKS:
* Pat Walters's blog post about structural alerts: practicalcheminformatics.blogspot.com/2018/08/filtering-chemical-libraries.html
* List of structural alerts used here (credits to Pat Walters): raw.githubusercontent.com/PatWalters/rd_filters/master/rd_filters/data/alert_collection.csv
* ChEMBL blog posts with links to other structural alerts: chembl.blogspot.com/2015/02/chembl-20-released.html


All websites have been accessed in April 2022

Options

OPTIONAL: Should 2D coordinates be (re-)generated?
If checked, the 2D coordinates of the input molecules will be (re-)calculated. Lacking or flawed coordinates might impair the component's functionality.
Please select the input column containing the molecules
Allowed data types are SMILES, Mol, SDF or RDKit molecule.
OPTIONAL: Choose the rule set you want to use for structural alerts
Please check the component description for more information on individual rule sets.

Input Ports

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Table containing chemical data in SMILES, SDF or Mol format.

Output Ports

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Input data containing valid molecules, plus columns containing the flag(s). If the input molecules match a structural alert from the chosen list(s), the first matching substructure is returned.
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Input molecules that could not be converted to a RDKit molecule.

Nodes

Extensions

Links

Download

To use this component in KNIME, download it from the below URL and open it in KNIME:

Download Component
On NodePit since: 2022-04-28
Last update: 2024-04-26
Created with KNIME version: v4.5.2

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