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KnowYourMolecule

Example workflow using the ChEMBL web services nodes.Performs a similarity search against ChEMBL and then retrieves, filters, summarises and produces filesfor analysis by molecular spreadsheet.For more information on the original spreadhseet see: https://www.ebi.ac.uk/chembldb/index.php/ws 2. File of actives in infrequent target names 2. File of actives in frequent target names 2. File of weak or inactive data 2. File of actives with activity type NOT equal to IC50, Ki, EC50, XC50 1. Double click &sketch one ormore similarmolecules here You can leave these alone 3. double click tochoose substructureor similarity:For similarity cutoff -suggest start with 75 OPTION B4. Manually select compounds you DON'T want pharmacology on (if all compounds are of interest you may want to try alower similarity cutoff at step 3)1. right click & select View: RD Kit interactive table2. Hilite/Clear hilite3. CTRL click to select a set of compounds for inclusion or exclusion4. Hilite: Hilite selected5. Close node & connect the upper (to annotate the selected compounds withbiological data) or the lower (to annotate unselected compounds) output fromthe Hilite row filter to the ChEMBL biology data lookup6. Click double white arrow in green circle to execute remainder of workflow Know Your MoleculeFind pharmacology associated with similar compoundsto yours from within ChEMBL OPTION A (default)4A. Select similar compounds based on tanimoto similarity cutoff - currently set to 0.41. right click & examine the filtered & non-filtered compounds2. double click the row filter and adjust the tanimoto cutoff value to adjust as required3. Click double white arrow in green circle to execute remainder of workflow 2. NEW - Full output without filteror pAct calculationQuerystructure searchNode 64Node 79Node 87Node 88Node 89Node 90Node 92Node 97Node 8786Node 8787Node 8789Node 8790 MarvinSketch ChEMBLdbConnector Input QC Filters CSV Writer CSV Writer write_pAct_files CSV Writer CSV Writer HiLite Row Splitter RDKit InteractiveTable Morgan sim Row Filter ChEMBL biologydata lookup CSV Writer Example workflow using the ChEMBL web services nodes.Performs a similarity search against ChEMBL and then retrieves, filters, summarises and produces filesfor analysis by molecular spreadsheet.For more information on the original spreadhseet see: https://www.ebi.ac.uk/chembldb/index.php/ws 2. File of actives in infrequent target names 2. File of actives in frequent target names 2. File of weak or inactive data 2. File of actives with activity type NOT equal to IC50, Ki, EC50, XC50 1. Double click &sketch one ormore similarmolecules here You can leave these alone 3. double click tochoose substructureor similarity:For similarity cutoff -suggest start with 75 OPTION B4. Manually select compounds you DON'T want pharmacology on (if all compounds are of interest you may want to try alower similarity cutoff at step 3)1. right click & select View: RD Kit interactive table2. Hilite/Clear hilite3. CTRL click to select a set of compounds for inclusion or exclusion4. Hilite: Hilite selected5. Close node & connect the upper (to annotate the selected compounds withbiological data) or the lower (to annotate unselected compounds) output fromthe Hilite row filter to the ChEMBL biology data lookup6. Click double white arrow in green circle to execute remainder of workflow Know Your MoleculeFind pharmacology associated with similar compoundsto yours from within ChEMBL OPTION A (default)4A. Select similar compounds based on tanimoto similarity cutoff - currently set to 0.41. right click & examine the filtered & non-filtered compounds2. double click the row filter and adjust the tanimoto cutoff value to adjust as required3. Click double white arrow in green circle to execute remainder of workflow 2. NEW - Full output without filteror pAct calculationQuerystructure searchNode 64Node 79Node 87Node 88Node 89Node 90Node 92Node 97Node 8786Node 8787Node 8789Node 8790 MarvinSketch ChEMBLdbConnector Input QC Filters CSV Writer CSV Writer write_pAct_files CSV Writer CSV Writer HiLite Row Splitter RDKit InteractiveTable Morgan sim Row Filter ChEMBL biologydata lookup CSV Writer

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On NodePit since: 2020-05-14
Last update: 2024-04-26
Created with KNIME version: v3.1.1

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