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BDBBuilder

make Molecules make Fingerprints All Data Molecular Properties Workflow: BDBBuilderPurpose: Workflow that processes the BDBOriginal Table, generates molecular descriptors and CDK and RDKit fingerprints, and creates a KNIME Table for use by other workflows. Estimated runtimeduration of 3 hours.Directions: Open and configure the first node "CSV Reader". Point it to the latest BindingDB donwloaded dataset (ie: BindingDB_All_2015m2.tsv.zip). Open and configure the last node "Table Writer". Point it to a location to save BDBBuilder formatted file.CDK - StandardCDK - ExtendedCDK - PubChemCDK - MACCSRDKit - MorganRDKit - FeatMorganRDKit - AtomPairRDKit - Layeredwrite fingerprintsto diskallmake CDKmoleculeRDKitmake RDKit moleculeCDK - EStateRDKit - AvalonRDKit - RDKitRDKit - TorsionRDKit - MACCSget rid of "not OK"KI & IC50-> Doubleread TSV fileRDKit - Patternremove salts from RDKit moleculesremove saltsfrom CDK molecules Fingerprints Fingerprints Fingerprints Fingerprints RDKit Fingerprint RDKit Fingerprint RDKit Fingerprint RDKit Fingerprint Table Writer Column Filter Molecule to CDK Molecule Type Cast RDKit DescriptorCalculation RDKit From Molecule Fingerprints RDKit Fingerprint RDKit Fingerprint RDKit Fingerprint RDKit Fingerprint Rule Engine Row Filter String To Number CSV Reader RDKit Fingerprint Missing Value(deprecated) RDKit Salt Stripper Connectivity Column Rename make Molecules make Fingerprints All Data Molecular Properties Workflow: BDBBuilderPurpose: Workflow that processes the BDBOriginal Table, generates molecular descriptors and CDK and RDKit fingerprints, and creates a KNIME Table for use by other workflows. Estimated runtimeduration of 3 hours.Directions: Open and configure the first node "CSV Reader". Point it to the latest BindingDB donwloaded dataset (ie: BindingDB_All_2015m2.tsv.zip). Open and configure the last node "Table Writer". Point it to a location to save BDBBuilder formatted file.CDK - StandardCDK - ExtendedCDK - PubChemCDK - MACCSRDKit - MorganRDKit - FeatMorganRDKit - AtomPairRDKit - Layeredwrite fingerprintsto diskallmake CDKmoleculeRDKitmake RDKit moleculeCDK - EStateRDKit - AvalonRDKit - RDKitRDKit - TorsionRDKit - MACCSget rid of "not OK"KI & IC50-> Doubleread TSV fileRDKit - Patternremove salts from RDKit moleculesremove saltsfrom CDK moleculesFingerprints Fingerprints Fingerprints Fingerprints RDKit Fingerprint RDKit Fingerprint RDKit Fingerprint RDKit Fingerprint Table Writer Column Filter Molecule to CDK Molecule Type Cast RDKit DescriptorCalculation RDKit From Molecule Fingerprints RDKit Fingerprint RDKit Fingerprint RDKit Fingerprint RDKit Fingerprint Rule Engine Row Filter String To Number CSV Reader RDKit Fingerprint Missing Value(deprecated) RDKit Salt Stripper Connectivity Column Rename

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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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On NodePit since: 2019-07-12
Last update: 2024-11-23
Created with KNIME version: v3.7.1

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