Icon

W6_​Maximum_​common_​substructure

W6_Maximum_common_substructure
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 similaritiesor differences 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 compoundsNode 274Node 275Node 277 RDKit MoleculeHighlighting RDKit SubstructureFilter RDKit MCS Group Loop Start ConstantValue Column Table View Column Filter Table Rowto Variable Molecule Type Cast RDKit From Molecule CSV Reader WorkflowService Input WorkflowService Output Loop End 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 similaritiesor differences 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 compoundsNode 274Node 275Node 277 RDKit MoleculeHighlighting RDKit SubstructureFilter RDKit MCS Group Loop Start ConstantValue Column Table View Column Filter Table Rowto Variable Molecule Type Cast RDKit From Molecule CSV Reader WorkflowService Input WorkflowService Output Loop End

Nodes

Extensions

Links

Download

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

Download Workflow
Created by: dominique
Created at: 2019-07-15
On NodePit since: 2022-01-28
Last update: 2024-05-01
Created with KNIME version: v4.5.1
Tags: Maximum common substructure (MCS)FMCS algorithmTeachOpenCADD

Deploy, schedule, execute, and monitor your KNIME workflows locally, in the cloud or on-premises – with our brand new NodePit Runner.

Try NodePit Runner!