Following the development of a virtual machine (JCIM), the 3D-e-Chem team now published a series of building blocks (nodes) and recipes (workflows) that can support complex computer-aided drug discovery efforts. The 3D-e-Chem team consists of cheminformatics and bioinformatics researchers from Netherlands eScience Center, Vrije Universiteit Amsterdam, Radboudumc Nijmegen, and BioAxis Research, including Stefan Verhoeven (eScience) and Chris de Graaf (PI, VU Amsterdam).
These newly developed cheminformatics tools and workflows for KNIME (the leading open data analytics platform) integrate chemical, pharmacological, and structural information for the prediction of interactions between drug molecules and therapeutic protein targets. The modular setup of these computer-aided drug discovery workflows and the use of well-established standards enables researchers to re-use and customize these workflows for their own drug discovery projects.
The 3D-e-Chem software tools and applications thereof are described in a recent open access publication in ChemMedChem. All the building blocks (nodes) are readily available as a community contribution in KNIME. Moreover, the source code of the nodes is open and available on the 3D-e-Chem GitHub.