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Chemistry_​Manipulation_​and_​Visualization

01_Chemistry_basics

This workflow demonstrates basic cheminformatics functionality within KNIME Analytics platform:
Reading and writing various chemistry data formats; canonalization of chemical structures; duplicate filtering; descriptor calculation; interactive filtering on multiple properties
Training sets were collected from ChEMBLdb. Each set corresponds to a publication in which lipophilicity was determined experimentally

Chemistry_Manipulation_and_VisualizationThis workflow demonstrates basic cheminformatics functionality within KNIME Analytics platform: Reading and writing various chemistry data formats; canonalization of chemical structures; duplicate filtering; descriptor calculation; interactive filtering on multiple propertiesTraining sets were collected from ChEMBLdb and PubChem. Each set corresponds to a publication in which logD at pH7.4 was determined experimentally. Step 1. Read data from different sources Step 2. Preprocess and customize the data Step 3. Remove duplicates Step 4. Compute descriptors and filter data tabel on multiple properties Step 5.Save publicAID_686912_datatable_all.csvpublic686912_CIDsextract namein-houseCHEMBL3301363.csvon IDmol, id, value, tagnew_inhouseadd Tagadd Tagadd TagMolecule_IDLogDMolecule_IDLogDby Tagphyschempropertiessvg to png CSV Reader SDF Reader File Reader(Complex Format) Joiner RDKit From Molecule RDKit From Molecule Concatenate Column Filter Excel Reader Molecule Type Cast ConstantValue Column ConstantValue Column ConstantValue Column Column Rename Column Rename Column Rename RDKit From Molecule RDKit Salt Stripper DuplicateRow Filter RDKit Canon SMILES Color Manager RDKit DescriptorCalculation Visualize moleculeswith experimental data SDF Writer Table Writer Excel Writer Column Filter RDKit Moleculeto SVG Renderer to Image Chemistry_Manipulation_and_VisualizationThis workflow demonstrates basic cheminformatics functionality within KNIME Analytics platform: Reading and writing various chemistry data formats; canonalization of chemical structures; duplicate filtering; descriptor calculation; interactive filtering on multiple propertiesTraining sets were collected from ChEMBLdb and PubChem. Each set corresponds to a publication in which logD at pH7.4 was determined experimentally. Step 1. Read data from different sources Step 2. Preprocess and customize the data Step 3. Remove duplicates Step 4. Compute descriptors and filter data tabel on multiple properties Step 5.Save publicAID_686912_datatable_all.csvpublic686912_CIDsextract namein-houseCHEMBL3301363.csvon IDmol, id, value, tagnew_inhouseadd Tagadd Tagadd TagMolecule_IDLogDMolecule_IDLogDby Tagphyschempropertiessvg to png CSV Reader SDF Reader File Reader(Complex Format) Joiner RDKit From Molecule RDKit From Molecule Concatenate Column Filter Excel Reader Molecule Type Cast ConstantValue Column ConstantValue Column ConstantValue Column Column Rename Column Rename Column Rename RDKit From Molecule RDKit Salt Stripper DuplicateRow Filter RDKit Canon SMILES Color Manager RDKit DescriptorCalculation Visualize moleculeswith experimental data SDF Writer Table Writer Excel Writer Column Filter RDKit Moleculeto SVG Renderer to Image

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To use this workflow in KNIME, download it from the below URL and open it in KNIME:

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Created by: daria_knime
Created at: 2018-05-03
On NodePit since: 2022-04-19
Last update: 2024-04-27
Created with KNIME version: v4.5.2
Tags: ChemistryInteractive ViewLife SciencesEducation

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