Download KNIME Workflows

ChemAxon KNIME Workflows

Various example workflows showing how ChemAxon tools can be used within KNIME
Minimum required KNIME version: 2.8.2 JChem Extensions version: v204 using JChem 6.3.0

Contents of the package

Reaction based enumeration
Virtual compound library design is an essential part of ligand-based drug design. It can be approached by putting together virtual reaction steps in order to generate a library that is likely to be synthetised using common common pathways.
Scaffold based enumeration
Another way of creating a virtual compound library is taking a core structure or scaffold, sets of R-groups and build compunds from them. In this workflow it is done by using our Markush technology to create generic structure of the library and enumerate explicit structures.
Molecule descriptors
It is important to predict physico-chemical properties and generate other descriptors for virtual libraries. With them one can achieve a better understanding of the relationship of chemical structures and their properties.
Clustering with KNIME
Calculate fingerprints with ChemAxon and do clustering with KNIME nodes.
Duplicate filtering
Removes duplicate structures. It contains a prefiltering step that makes the workflow fast if there isn’t too much duplicates.

Old Workflow Examples and Dataset