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Work-Flow-no-4-Read-Calculate-Plot-Neuraminidase-initial-data 6

WORKFLOW 4 (ADDITIONAL EXAMPLE not discussed in manuscript)Example of reading a fully expanded ChEMBL target-extracted file with the affinity data for Neuraminidase. Added seven columns: PSAoverMW, BEI, SEI, NBEI, NSEI, nBEI and mBEI and plotted with 2D/3D scatterplot or Simple Scatter Plot for comparison. Computed descriptors with the RDKit Descriptor calculators and added columns (NHEA, NPOL(N+O)-Lipinski)) and MW, TPSA. Then added the nodes to do the algebraand the scatter plot node to plot the columns of choice to produce a 'MiniAtlasCBS' for that target. ==@The data could be selected (Ki vis. IC50, Kd etc) as needed to plot only subsets (e.g. retaining only IC50 and Ki) using the Table validator module.@The input data file is in *.txt mode. Input file: Neuraminidase-15_21_03-21.txt @Tested by C.A-Z for deposition at the KNIME workflow examples website, Sept. 17.2015.@ 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 by Dr.Azat Mukhametov. Publisher VENTURE Pharmaceuticals, Austin Publishing Group. Publication, 2016. Node 210PSA/MWBEISEISMILEStoStructureProperty Cal.NBEINSEInBEImBEINode 12 File Reader Scatter Plot Math Formula Math Formula Math Formula Molecule Type Cast RDKit DescriptorCalculation Math Formula Math Formula Math Formula Math Formula 2D/3D Scatterplot WORKFLOW 4 (ADDITIONAL EXAMPLE not discussed in manuscript)Example of reading a fully expanded ChEMBL target-extracted file with the affinity data for Neuraminidase. Added seven columns: PSAoverMW, BEI, SEI, NBEI, NSEI, nBEI and mBEI and plotted with 2D/3D scatterplot or Simple Scatter Plot for comparison. Computed descriptors with the RDKit Descriptor calculators and added columns (NHEA, NPOL(N+O)-Lipinski)) and MW, TPSA. Then added the nodes to do the algebraand the scatter plot node to plot the columns of choice to produce a 'MiniAtlasCBS' for that target. ==@The data could be selected (Ki vis. IC50, Kd etc) as needed to plot only subsets (e.g. retaining only IC50 and Ki) using the Table validator module.@The input data file is in *.txt mode. Input file: Neuraminidase-15_21_03-21.txt @Tested by C.A-Z for deposition at the KNIME workflow examples website, Sept. 17.2015.@ 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 by Dr.Azat Mukhametov. Publisher VENTURE Pharmaceuticals, Austin Publishing Group. Publication, 2016. Node 210PSA/MWBEISEISMILEStoStructureProperty Cal.NBEINSEInBEImBEINode 12 File Reader Scatter Plot Math Formula Math Formula Math Formula Molecule Type Cast RDKit DescriptorCalculation Math Formula Math Formula Math Formula Math Formula 2D/3D Scatterplot

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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: v3.7.1

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