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Matched Molecular Pairs Analysis

Matched Molecular Pair analysis

This workflow demonstrates how to to matched molecular pair analysis in KNIME and proposes a way how to deal with biological assay data that includes a qualifer. The data has been retrieved from ChEMBL27 and contains Ki values of hERG. The human ether-à-go-go-related gene (hERG) product is a potassium channel whose inhibition can cause potential lethal cardiac arrythmia, so introducing transformations to drug candidates that reduce hERG inhibition is desired.

As MMP analysis results in a range of values, we will take the median to select transformations to investigate further. The Interactive View contains a table with all transformations that match the criteria defined by the user. When a transformation is selected, the details show up in a second table underneath.

Matched Molecular Pairs analysis on hERG inhibitor dataThe data has been retrieved from ChEMBL27 and contains Ki values for hERG as a target. Ratio of pKi values and the resulting qualifiers: =L =R -> =L-R>L =R -><L-R=L >R ->>L-R>L >R -> undefined Molecule preprocessing Finding matched molecular pairs Introducing thequalifier of individualdifferences/ratios Mind the logarithm: 0.3 -> ~2-fold change 0.5 -> ~3-fold change 0.7 -> ~5-fold change 1 -> 10-fold change 2 -> 100-fold change upper port: all transformationmatching the user-definedfilter criterialower port: table with detailsof the transformation/MMPchosen in the Interactive View fragmentationfind MMPon preprocessed moleculegroup on SMILEScalculate missing pChEMBLvalues (-log(M) of Ki) filter out missingstandardvalues (=Ki value)* minimum number of pairs* increase or decrease in Ki* threshold / change in median KiFile Reader Speedy SMILESDe-salt Speedy SMILES StripStereochemistry Speedy SMILES StripDouble Bond Geometry MMP MoleculeFragment (RDKit) Fragments to MMPs DuplicateRow Filter GroupBy Column Filter Column Rename Math Formula Column Resorter Column Filter Rule Engine Investigate MMPs RDKit Canon SMILES Row Splitter Configure theresults of choice Matched Molecular Pairs analysis on hERG inhibitor dataThe data has been retrieved from ChEMBL27 and contains Ki values for hERG as a target. Ratio of pKi values and the resulting qualifiers: =L =R -> =L-R>L =R -><L-R=L >R ->>L-R>L >R -> undefined Molecule preprocessing Finding matched molecular pairs Introducing thequalifier of individualdifferences/ratios Mind the logarithm: 0.3 -> ~2-fold change 0.5 -> ~3-fold change 0.7 -> ~5-fold change 1 -> 10-fold change 2 -> 100-fold change upper port: all transformationmatching the user-definedfilter criterialower port: table with detailsof the transformation/MMPchosen in the Interactive View fragmentationfind MMPon preprocessed moleculegroup on SMILEScalculate missing pChEMBLvalues (-log(M) of Ki) filter out missingstandardvalues (=Ki value)* minimum number of pairs* increase or decrease in Ki* threshold / change in median KiFile Reader Speedy SMILESDe-salt Speedy SMILES StripStereochemistry Speedy SMILES StripDouble Bond Geometry MMP MoleculeFragment (RDKit) Fragments to MMPs DuplicateRow Filter GroupBy Column Filter Column Rename Math Formula Column Resorter Column Filter Rule Engine Investigate MMPs RDKit Canon SMILES Row Splitter Configure theresults of choice

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

Download Workflow
Created by: alice.krebs
Created at: 2020-12-18
On NodePit since: 2021-05-25
Last update: 2026-01-13
Created with KNIME version: v4.3.2
Tags: Life SciencesCheminformaticsMatched Molecular PairsQualifiers

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