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20210428_​Pikairos_​Similarity_​Distance_​RDKIT_​Alternative

Optimizing a workflow analyzing the similarity distance to the nearest neighbour in a compound library

DataCurrently storedlocally in workflowatknime://knime.workflow/_LOCAL_DATA/Covalent_Cys_41378.sdfConvert Moleculesto RDKit formatCalculate MorganFingerprints(EFCP-like)but chose here whatfits best to your problemTanimoto similaritywith 1 as identicaland 0 completelydifferent moleculesI chose here the two NNsince one is the molecule itselfgiven that we are comparingmolecules intraset(two input ports with same data)RowID (with smiles) is usedas NN molecule referenceCalculateCanonical SmilesSet the RowIDwith Canonical SmilesKeep onlythe found NN moleculedifferent to the referenceCast NN molecule referenceas moleculeThe NN moleculefor the whole setSDF Reader RDKit From Molecule RDKit Fingerprint Similarity Search RDKit Canon SMILES RowID Row Filter Molecule Type Cast InteractiveTable (local) DataCurrently storedlocally in workflowatknime://knime.workflow/_LOCAL_DATA/Covalent_Cys_41378.sdfConvert Moleculesto RDKit formatCalculate MorganFingerprints(EFCP-like)but chose here whatfits best to your problemTanimoto similaritywith 1 as identicaland 0 completelydifferent moleculesI chose here the two NNsince one is the molecule itselfgiven that we are comparingmolecules intraset(two input ports with same data)RowID (with smiles) is usedas NN molecule referenceCalculateCanonical SmilesSet the RowIDwith Canonical SmilesKeep onlythe found NN moleculedifferent to the referenceCast NN molecule referenceas moleculeThe NN moleculefor the whole setSDF Reader RDKit From Molecule RDKit Fingerprint Similarity Search RDKit Canon SMILES RowID Row Filter Molecule Type Cast InteractiveTable (local)

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Created by: Molina
Created at: 2021-04-28
On NodePit since: 2022-02-06
Last update: 2024-04-27
Created with KNIME version: v4.2.4
Tags: RDKITPIKAIROS

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