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Work-Flow-no-2-ChEMBL-data-extractor-AtlasCBS-DHRF-human

WORFLOW2 (discussed in manuscript) General extract based on target name/number and later submitted query again to extract compounds active against that target and some compound properties. =Tables combined to a set of unique Chembl_IDs for further processing.Added a 'Row Splitter' to select data according to a certain criteria; in the example assay_type: Binding vs. Functional. This can be changed to selectthe appropriate assay data. Other 'row splitters' have been added to select Ki's vs. others and then again to extract IC50's from the remainder ones.LEIs are computed and plotted using Scatter 2D/3D plots.=Certain properties are calculated with the RDKit Descriptor Calculation, 'String' for affinity value is converted to number for further calculationof the Ligand Efficiencies (LEIs). Six are calculated: BEI, SEI, NBEI, NSEI, nBEI, mBEI (consult references for definitions). In addition, the ratio of BEI/SEI is also calculated as it isequal to BEI/SEI = 10*(PSA/MW); This variable is called: PSAoverMW. Other Ligand Efficiency Metrics can be easily calculated and added to theTable for further plotting, using the 2D/3D Scatter plot.= @Written by C.A-Z with the help of G. Papadanatos at EBI, during the visit of C.AZ to EBI, March 9-17, 2015. @Tested April 15.2015. for the VEGFR2 (CHEMBL target ID 279) data. It worked fine for over 7000 entries. 6400 or so with IC50s Upper flow, and 260 or so Ki, lower track.Tested by C.A-Z for deposition in the KNIME workflow examples site Node 4Node 5Node 6Node 7Node 8Node 9Pchembl-valueNode 11Node 12PSAoverMWBEISEINBEINSEInBEImBEISelect assay BvsFKi vs othersSelect IC50Pchembl-valueBEISEINBEINSEInBEImBEINode 30PSAoverMWChEMBLdb Connector ChEMBLdbConnector Input Joiner GroupBy Molecule Type Cast RDKit DescriptorCalculation Math Formula 2D/3D Scatterplot String To Number Math Formula Math Formula Math Formula Math Formula Math Formula Math Formula Math Formula Row Splitter Row Splitter Row Splitter Math Formula Math Formula Math Formula Math Formula Math Formula Math Formula Math Formula 2D/3D Scatterplot Math Formula WORFLOW2 (discussed in manuscript) General extract based on target name/number and later submitted query again to extract compounds active against that target and some compound properties. =Tables combined to a set of unique Chembl_IDs for further processing.Added a 'Row Splitter' to select data according to a certain criteria; in the example assay_type: Binding vs. Functional. This can be changed to selectthe appropriate assay data. Other 'row splitters' have been added to select Ki's vs. others and then again to extract IC50's from the remainder ones.LEIs are computed and plotted using Scatter 2D/3D plots.=Certain properties are calculated with the RDKit Descriptor Calculation, 'String' for affinity value is converted to number for further calculationof the Ligand Efficiencies (LEIs). Six are calculated: BEI, SEI, NBEI, NSEI, nBEI, mBEI (consult references for definitions). In addition, the ratio of BEI/SEI is also calculated as it isequal to BEI/SEI = 10*(PSA/MW); This variable is called: PSAoverMW. Other Ligand Efficiency Metrics can be easily calculated and added to theTable for further plotting, using the 2D/3D Scatter plot.= @Written by C.A-Z with the help of G. Papadanatos at EBI, during the visit of C.AZ to EBI, March 9-17, 2015. @Tested April 15.2015. for the VEGFR2 (CHEMBL target ID 279) data. It worked fine for over 7000 entries. 6400 or so with IC50s Upper flow, and 260 or so Ki, lower track.Tested by C.A-Z for deposition in the KNIME workflow examples site Node 4Node 5Node 6Node 7Node 8Node 9Pchembl-valueNode 11Node 12PSAoverMWBEISEINBEINSEInBEImBEISelect assay BvsFKi vs othersSelect IC50Pchembl-valueBEISEINBEINSEInBEImBEINode 30PSAoverMWChEMBLdb Connector ChEMBLdbConnector Input Joiner GroupBy Molecule Type Cast RDKit DescriptorCalculation Math Formula 2D/3D Scatterplot String To Number Math Formula Math Formula Math Formula Math Formula Math Formula Math Formula Math Formula Row Splitter Row Splitter Row Splitter Math Formula Math Formula Math Formula Math Formula Math Formula Math Formula Math Formula 2D/3D Scatterplot Math Formula

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Created by: gabriel
Created at: 2014-07-07
On NodePit since: 2019-07-12
Last update: 2024-11-21
Created with KNIME version: v2.11.2.0046103

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