The 3D-e-Chem nodes have been developed as part of the 3D-e-Chem project by Vrije Universiteit Amsterdam, Radboudumc Nijmegen and Netherlands eScience Center. The nodes complement existing cheminformatics and bioinformatics nodes to enable the efficient exploitation of structural and pharmacological protein-ligand interaction data from proteome-wide databases, as well as customized information systems focused on e.g. G Protein-Coupled Receptors (GPCRdb) and protein kinases (KLIFS). The 3D-e-Chem KNIME node toolbox provides building blocks for the design of flexible computer-aided drug discovery workflows, including ligand-based metabolism prediction (SyGMA), sequence analyses (ss-TEA), and structure-based protein binding site comparison and bioisosteric replacement for ligand design (KRIPO). The open source, freely available Virtual Machine, 3D-e-Chem-VM facilitates the efficient use of pre-configured 3D-e-Chem tools and other resources.
Current 3D-e-Chem nodes have been grouped as follows:
The GitHub repository of each node has a simple example workflow, including:
Any questions about the nodes can be posted on the 3D-e-Chem KNIME forum. Several example workflows have been described in the 3D-e-Chem application note, and a list of 3D-e-Chem workflows can be found here.
The 3D-e-Chem project, involving the Vrije Universiteit Amsterdam, Radboudumc Nijmegen and Netherlands eScience Center, develops technologies to improve the integration of ligand and protein data for structure-based prediction of protein-ligand selectivity and polypharmacology. The project uses the KNIME Analytics Platform to integrate different structural cheminformatics and bioinformatics technologies and datasets.
The source code can be accessed at https://github.com/3D-e-Chem. Each node has its own repository, for example, https://github.com/3D-e-Chem/knime-gpcrdb contains the source code for the GPCRDB nodes.
The 3D-e-Chem nodes are released under GNU GPL version 3 license.