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Work-Flow-no-3-Read-CSV-Calculate-Merge-ChEMBL-target-view 1

WORKFLOW 3 (discussed in Manuscript)This workflow allows the user to extract from the ChEMBL database the data fora certain target as given by the 'Target_ChemblID (Neuraminidase is used: CHEMBL2051),with compounds and bioactivites on the upper pipeline. On the lower pipeline the user provides a 'UserdataSet' containingCompound ID, smiles, Bioactivity Type (IC50), value (in nM units), Target-ID (CHEMBL2051). File provided 11HSD_test.csv (from WORKFLOW 1). Target ID provided with this data set CHEMBL2051 is 'arbitrary' andshould be identical to the one extracted from the ChEMBL database to compare 'proprietary data' with data available in ChEMBLfor the same target. =These two data sets are combined using the 'Concatenate' Node and later used for plottingin Ligand Efficiency planes, using the AtlasCBS framework. In this case, the 'Row Splitter' nodeis used to select from all the ChEMBL data for Neuraminidase, only the one with a well defined IC50 value (IC50= to a decimal) .=These data are easily complemented with the calculation of several additional variables/columns: PSAoverMW = (10*PSA/MW): ratio of BEI/SEI; useful to follow the polarity of the compounds BEI = pIC50/(MW in KiloDaltons) = pIC50/(MW*0.001) SEI = pIC50/(PSA*0.01) (Polar surface area in 100th units)NBEI = pIC50/NHEANSEI = pIC50/NPOL (=N+O count). nBEI = -log [(pIC50/NHEA)= pIC50 + log(NHEA) mBEI = -log[(pIC50/MW)= pIC50+ log(MW).=These variables are available to plot with the Scatter 2D/3D plots.====@This workflow prepared by C.A-Z with the help of George Papadatos at EBI during the visitof CAZ at EBI, March 9-17, 2015).@Tested by C.A-Z for deposition at the KNIME workflow example site.===@ Further details of the application an use of this workflow will be published in:'AtlasCBS: A Graphic Tool to Map the Content of Structure-Activity Databases' by C. Abad-Zapatero in 'Software and Techniques ofr Biomolecular Modeling' Edited byDr. Azat Mukhametov. Publisher VENTURE Pharmaceuticals, Austin Publishing Group. Publication, 2016. 10PSA/MW3D-plotsmiles string to structure Property Cal.Node 7convert to nM unitJoin ChEMBL with external dataBEISEINode 15Select IC50Node 18Node 19Node 20Convert to no.NBEINSEInBEImBEINode 29Node 30File Reader Math Formula 2D/3D Scatterplot Molecule Type Cast RDKit DescriptorCalculation GroupBy Math Formula Concatenate Math Formula Math Formula String To Number Row Splitter ChEMBLdb Connector Joiner ChEMBLdbConnector Input Math Formula Math Formula Math Formula Math Formula Math Formula Number To String Column Rename WORKFLOW 3 (discussed in Manuscript)This workflow allows the user to extract from the ChEMBL database the data fora certain target as given by the 'Target_ChemblID (Neuraminidase is used: CHEMBL2051),with compounds and bioactivites on the upper pipeline. On the lower pipeline the user provides a 'UserdataSet' containingCompound ID, smiles, Bioactivity Type (IC50), value (in nM units), Target-ID (CHEMBL2051). File provided 11HSD_test.csv (from WORKFLOW 1). Target ID provided with this data set CHEMBL2051 is 'arbitrary' andshould be identical to the one extracted from the ChEMBL database to compare 'proprietary data' with data available in ChEMBLfor the same target. =These two data sets are combined using the 'Concatenate' Node and later used for plottingin Ligand Efficiency planes, using the AtlasCBS framework. In this case, the 'Row Splitter' nodeis used to select from all the ChEMBL data for Neuraminidase, only the one with a well defined IC50 value (IC50= to a decimal) .=These data are easily complemented with the calculation of several additional variables/columns: PSAoverMW = (10*PSA/MW): ratio of BEI/SEI; useful to follow the polarity of the compounds BEI = pIC50/(MW in KiloDaltons) = pIC50/(MW*0.001) SEI = pIC50/(PSA*0.01) (Polar surface area in 100th units)NBEI = pIC50/NHEANSEI = pIC50/NPOL (=N+O count). nBEI = -log [(pIC50/NHEA)= pIC50 + log(NHEA) mBEI = -log[(pIC50/MW)= pIC50+ log(MW).=These variables are available to plot with the Scatter 2D/3D plots.====@This workflow prepared by C.A-Z with the help of George Papadatos at EBI during the visitof CAZ at EBI, March 9-17, 2015).@Tested by C.A-Z for deposition at the KNIME workflow example site.===@ Further details of the application an use of this workflow will be published in:'AtlasCBS: A Graphic Tool to Map the Content of Structure-Activity Databases' by C. Abad-Zapatero in 'Software and Techniques ofr Biomolecular Modeling' Edited byDr. Azat Mukhametov. Publisher VENTURE Pharmaceuticals, Austin Publishing Group. Publication, 2016. 10PSA/MW3D-plotsmiles string to structure Property Cal.Node 7convert to nM unitJoin ChEMBL with external dataBEISEINode 15Select IC50Node 18Node 19Node 20Convert to no.NBEINSEInBEImBEINode 29Node 30File Reader Math Formula 2D/3D Scatterplot Molecule Type Cast RDKit DescriptorCalculation GroupBy Math Formula Concatenate Math Formula Math Formula String To Number Row Splitter ChEMBLdb Connector Joiner ChEMBLdbConnector Input Math Formula Math Formula Math Formula Math Formula Math Formula Number To String Column Rename

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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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