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BDBBuilderFast

Workflow: BDBBuilderFastPurpose: Workflow that processes the BDBOriginal Table, generates RDKit fingerprints, and creates a KNIME Table for use by other workflows. Estimated runtime duration of 30 minutes.Directions: Open and configure the first node "CSV Reader". Point it to the latest BindingDB downloaded dataset (ie: BindingDB_All_2015m2.tsv.zip). By default, an accompanying dataset is used.Open and configure the last node "Table Writer". Point it to a location to save BDBBuilderFast formatted file. Run workflow.Write Fingerprint Table to DiskKeep only pertinent fieldsConvert to SMILESMake RDKit moleculesGenerate RDKit/RDKitfingerprintsFlag inappropriate entriesGet rid of "not OK"KI & IC50-> DoubleRead TSV fileRemove missing entriesRemove saltsUse multipleprocessor cores Table Writer Column Filter Molecule Type Cast RDKit From Molecule RDKit Fingerprint Rule Engine Row Filter String To Number CSV Reader Missing Value(deprecated) RDKit Salt Stripper Parallel Chunk End ParallelChunk Start Workflow: BDBBuilderFastPurpose: Workflow that processes the BDBOriginal Table, generates RDKit fingerprints, and creates a KNIME Table for use by other workflows. Estimated runtime duration of 30 minutes.Directions: Open and configure the first node "CSV Reader". Point it to the latest BindingDB downloaded dataset (ie: BindingDB_All_2015m2.tsv.zip). By default, an accompanying dataset is used.Open and configure the last node "Table Writer". Point it to a location to save BDBBuilderFast formatted file. Run workflow.Write Fingerprint Table to DiskKeep only pertinent fieldsConvert to SMILESMake RDKit moleculesGenerate RDKit/RDKitfingerprintsFlag inappropriate entriesGet rid of "not OK"KI & IC50-> DoubleRead TSV fileRemove missing entriesRemove saltsUse multipleprocessor coresTable Writer Column Filter Molecule Type Cast RDKit From Molecule RDKit Fingerprint Rule Engine Row Filter String To Number CSV Reader Missing Value(deprecated) RDKit Salt Stripper Parallel Chunk End ParallelChunk Start

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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: 2024-11-18
Created with KNIME version: v3.7.1

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