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.Publication in Journal of Chemical Information and Modeling (JCIM): link
The 3D-e-Chem team consists of cheminformatics and bioinformatics researchers from the Radboud university medical center, eScience Center, BioAxis Research, and Vrije Universiteit Amsterdam, including Albert Kooistra, Ross McGuire, and Gert Vriend from the Centre for Molecular and Biomolecular Informatics and Chris de Graaf (PI) from 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.
Related news items
Radboudumc research most lungs recover well after COVID-1926 November 2020
In severe COVID-19 patients the lung tissue recovers well in most cases. This is shown in research by the Radboudumc, published in Clinical Infectious Diseases. Striking conclusion: patients who were referred by the general practitioner recover worse than ICU patients.read more
Marianne Boenink has been appointed professor in Ethics of Healthcare26 November 2020
Health scientist and philosopher Marianne Boenink has been appointed professor in Ethics of Healthcare at the Radboud University/ Radboudumc, as of 1 August 2020.read more
The effects of the COVID-19 pandemic on (future) parents and their babies26 November 2020
While the corona crisis affects all of us, people who have just started a family or are trying to, are doing this in a sub-optimal situation. Researchers are trying to find out how the ongoing crisis is affecting them.read more
Hydroxychloroquine against malaria appears to block 'trained immunity'25 November 2020
Raphaël Duivenvoorden and colleagues have discovered an as yet unknown effect of hydroxychloroquine, which are published in Cell Reports Medicine.read more