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(3D) Fragment library design workflow v1.1

HOW TO USEGreen nodes: "Execute and open views" → Setup → Close and apply changesYellow nodes: Double-click to setup → "Execute"Grey nodes: See description below node• See individual nodes' description for more details• Within certain components, some nodes are highlighted with a red box. Thesenodes are usually tables that can be expanded or contain standard settings (e.g., atable containing the reaction types and cooresponding SMARTS) https://pubs.acs.org/doi/10.1021/acsmedchemlett.2c00503 UPDATE LOG v1.1- Bug fix w.r.t. protecting groups- Outdated connection to PubChem fixedLast tested on 20-03-2024 in KNIME 3.4.1 Open metanodeto configureLoad databasewith reactantsCarbamatesOpen componentand configure step-by-stepv1 Prepare Reactants Functional GroupSelection SDF Reader Filter products Filter Reactants Reactor GenerateConformations Novelty filter 3D filter Clustering Compound picking HOW TO USEGreen nodes: "Execute and open views" → Setup → Close and apply changesYellow nodes: Double-click to setup → "Execute"Grey nodes: See description below node• See individual nodes' description for more details• Within certain components, some nodes are highlighted with a red box. Thesenodes are usually tables that can be expanded or contain standard settings (e.g., atable containing the reaction types and cooresponding SMARTS) https://pubs.acs.org/doi/10.1021/acsmedchemlett.2c00503 UPDATE LOG v1.1- Bug fix w.r.t. protecting groups- Outdated connection to PubChem fixedLast tested on 20-03-2024 in KNIME 3.4.1 Open metanodeto configureLoad databasewith reactantsCarbamatesOpen componentand configure step-by-stepv1 Prepare Reactants Functional GroupSelection SDF Reader Filter products Filter Reactants Reactor GenerateConformations Novelty filter 3D filter Clustering Compound picking

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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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Created by: vu
Created at: 2021-02-02
On NodePit since: 2025-03-21
Last update: 2025-03-25
Created with KNIME version: v4.3.1

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