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05_​Working_​In_​3D

Working in 3D

This workflow demonstrates use of some of the RDKit's 3D functionality, including 2D->3D conversion and geometry optimization.

The dataset used in this example workflow was taken from the PDB (http://www.rcsb.org/pdb/home/home.do).

Requirements:
- RDKit Community Nodes
- KNIME Python integration and an RDKit Python installation.

Shows some basic 3D functionality with the RDKit nodesExtensions required:RDKitKNIME Python integration (including an RDKit python install) Generate conformations Calculate RMS to xtal structure Compare to minimized structures ligand 0HKfrom structure 4u15(spiriva)keep the firstmoleculeGenerate 50conformationsNode 5Node 6Calc RMSD of conformersto original structureLook at a histogramof RMSD valuesMMFF94 MinimizationNode 10Calc RMSD of conformersto original structureNode 12Node 13Node 14Sort by RMSD SDF Reader Row Filter RDKit AddConformers RDKit Add Hs RDKit Remove Hs Python Script (1⇒1) Histogram(interactive) RDKit OptimizeGeometry RDKit Remove Hs Python Script (1⇒1) Column Rename Joiner JavaScriptScatter Plot Sorter Shows some basic 3D functionality with the RDKit nodesExtensions required:RDKitKNIME Python integration (including an RDKit python install) Generate conformations Calculate RMS to xtal structure Compare to minimized structures ligand 0HKfrom structure 4u15(spiriva)keep the firstmoleculeGenerate 50conformationsNode 5Node 6Calc RMSD of conformersto original structureLook at a histogramof RMSD valuesMMFF94 MinimizationNode 10Calc RMSD of conformersto original structureNode 12Node 13Node 14Sort by RMSDSDF Reader Row Filter RDKit AddConformers RDKit Add Hs RDKit Remove Hs Python Script (1⇒1) Histogram(interactive) RDKit OptimizeGeometry RDKit Remove Hs Python Script (1⇒1) Column Rename Joiner JavaScriptScatter Plot Sorter

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: 2016-12-19
On NodePit since: 2019-07-12
Last update: 2026-02-12
Created with KNIME version: v3.3.0

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