Icon

Database substructure search

Substructure search dashboard

This workflow demonstrates how to do substructure search on a sqlite data base. The input substructure can be given in SMILES and then modified in the sketcher, or directly be drawn in the sketcher. The molecules matching the substructure are shown in an interactive view with the substructure highlighted. Several slider filter widgets allow further filtering of molecules. The resulting molecules can be downloaded as Excel file.

Connect to SQLiteRead from table "cmpds"SMILES -> SDFmake it "data"string -> SMILESactually not needed,hopefully the SMILES in the DB are canonicalizedUse SMARTS to do a substructuresearchhighlight the matching atomsmake the molecule from sketcher "data"string -> SDFmake it an RDKit moleculeRDKit -> SMARTSSQLite Connector DB Query Reader RDKit To Molecule Variable toTable Row Molecule Type Cast Table Rowto Variable Download File RDKit Canon SMILES Renderer to Image RDKit SubstructureFilter RDKit MoleculeHighlighting Table Rowto Variable Table viewof compounds Variable toTable Row Molecule Type Cast SMILES input Sketcher RDKit From Molecule RDKit To Molecule Molecule Type Cast Excel Writer Configure file name Connect to SQLiteRead from table "cmpds"SMILES -> SDFmake it "data"string -> SMILESactually not needed,hopefully the SMILES in the DB are canonicalizedUse SMARTS to do a substructuresearchhighlight the matching atomsmake the molecule from sketcher "data"string -> SDFmake it an RDKit moleculeRDKit -> SMARTSSQLite Connector DB Query Reader RDKit To Molecule Variable toTable Row Molecule Type Cast Table Rowto Variable Download File RDKit Canon SMILES Renderer to Image RDKit SubstructureFilter RDKit MoleculeHighlighting Table Rowto Variable Table viewof compounds Variable toTable Row Molecule Type Cast SMILES input Sketcher RDKit From Molecule RDKit To Molecule Molecule Type Cast Excel Writer Configure file name

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: glandrum
Created at: 2015-02-07
On NodePit since: 2022-05-17
Last update: 2024-11-21
Created with KNIME version: v4.3.2
Tags: Life ScienceCheminformaticsWebportal

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

Try NodePit Runner!