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04_​Matched Molecular Pairs

04_Matched Molecular Pairs This workflow demonstrates Matched Molecular Pairs (MMP) analysis. After the data is read in, we filter out the fingerprint columns and remove compounds without clearly defined Ki values. Then we proceed with data preprocessing, which includes de-salting,stripping of stereochemistry and double bond geometry. Exercise1. De-salt the SMILES strings using the Speedy SMILES De-salt node 2. Strip out defined stereocenters using the Speedy SMILES Strip Stereochemistry node3. Strip out defined double bond geometries using the Speedy SMILES Strip Double Bond Geometry node4. Canonicalize the pre-processed SMILES5. Check for duplicates 6. Fragment the molecules using the MMP Molecule Fragment (RDKit) node7. Find the matched molecular pairs within the fragments using the Fragments to MMPs node8. Use a GroupBy node after the Column Resorter to find how many pairs are associated with each transformation9. Use optionally a Column Resorter and a Column Rename node to clean the data and create an interactive view of your choice to visualize the MMPs Nr ofoccurencesexclude missing standard values and Ki values defined as '>' or '<' Column Rename Column Resorter Table Reader Column Filter Rule-basedRow Filter 04_Matched Molecular Pairs This workflow demonstrates Matched Molecular Pairs (MMP) analysis. After the data is read in, we filter out the fingerprint columns and remove compounds without clearly defined Ki values. Then we proceed with data preprocessing, which includes de-salting,stripping of stereochemistry and double bond geometry. Exercise1. De-salt the SMILES strings using the Speedy SMILES De-salt node 2. Strip out defined stereocenters using the Speedy SMILES Strip Stereochemistry node3. Strip out defined double bond geometries using the Speedy SMILES Strip Double Bond Geometry node4. Canonicalize the pre-processed SMILES5. Check for duplicates 6. Fragment the molecules using the MMP Molecule Fragment (RDKit) node7. Find the matched molecular pairs within the fragments using the Fragments to MMPs node8. Use a GroupBy node after the Column Resorter to find how many pairs are associated with each transformation9. Use optionally a Column Resorter and a Column Rename node to clean the data and create an interactive view of your choice to visualize the MMPs Nr ofoccurencesexclude missing standard values and Ki values defined as '>' or '<' Column Rename Column Resorter Table Reader Column Filter Rule-basedRow Filter

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Created by: alice.krebs
Created at: 2020-12-18
On NodePit since: 2024-01-14
Last update: 2024-12-17
Created with KNIME version: v4.4.1

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