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TeachOpenCADD_​Workflow6_​Maximum_​common_​substructure

TeachOpenCADD Workflow 6: Maximum common substructures

In order to visualize shared scaffolds and thereby emphasize the extent and type of chemical similarities or differences of a compound cluster, the maximum common substructure (MCS) can be calculated and highlighted.
In this workflow, the MCS for the largest cluster from previously clustered compounds (TeachOpenCADD Workflow 5) is calculated using the FMCS algorithm.

Highlight substructures Step 1Show MCS for largest cluster using the FMCS algorithm This workflow is part of the TeachOpenCADD pipeline: https://hub.knime.com/volkamerlab/space/TeachOpenCADDRead more on the theoretical background of this workflow: https://projects.volkamerlab.org/teachopencadd/talktorials/T006_compound_maximum_common_substructures.html Find substructures Change RDKit MCS node properties:- Double click on "RDKit MCS" node- Currently set: - Threshold: 0,9 = in 90% is MCS present - Atom comparison: any - Bond comparison: orderThis workflow adapts the KNIME workflow example 0x1_Maximum_Common_Substructure (Daria Goldmann, KNIMEIntroduction and Training Session at Volkamer Lab in Berlin on 2019-01-21). Step 2Post-process table and output 6. Maximum common substructuresIn order to visualize shared scaffolds and thereby emphasize the extent and type of chemical similarities ordifferences of a compound cluster, the maximum common substructure (MCS) can be calculated andhighlighted. In this workflow, the MCS for the largest cluster from the previous workflow 4 is calculatedusing the FMCS algorithm. Highlight the atoms matching the coreFilter out molecules thatdo not match the MCSList of compoundsRDKit MoleculeHighlighting RDKit SubstructureFilter RDKit MCS Group Loop Start Loop End(deprecated) ConstantValue Column Table View Column Filter Table Rowto Variable Molecule Type Cast RDKit From Molecule CSV Reader Highlight substructures Step 1Show MCS for largest cluster using the FMCS algorithm This workflow is part of the TeachOpenCADD pipeline: https://hub.knime.com/volkamerlab/space/TeachOpenCADDRead more on the theoretical background of this workflow: https://projects.volkamerlab.org/teachopencadd/talktorials/T006_compound_maximum_common_substructures.html Find substructures Change RDKit MCS node properties:- Double click on "RDKit MCS" node- Currently set: - Threshold: 0,9 = in 90% is MCS present - Atom comparison: any - Bond comparison: orderThis workflow adapts the KNIME workflow example 0x1_Maximum_Common_Substructure (Daria Goldmann, KNIMEIntroduction and Training Session at Volkamer Lab in Berlin on 2019-01-21). Step 2Post-process table and output 6. Maximum common substructuresIn order to visualize shared scaffolds and thereby emphasize the extent and type of chemical similarities ordifferences of a compound cluster, the maximum common substructure (MCS) can be calculated andhighlighted. In this workflow, the MCS for the largest cluster from the previous workflow 4 is calculatedusing the FMCS algorithm. Highlight the atoms matching the coreFilter out molecules thatdo not match the MCSList of compoundsRDKit MoleculeHighlighting RDKit SubstructureFilter RDKit MCS Group Loop Start Loop End(deprecated) ConstantValue Column Table View Column Filter Table Rowto Variable Molecule Type Cast RDKit From Molecule CSV Reader

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