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
Radboud-led collaboration generates innovative candidate drug against malaria19 September 2019
A molecule once designed to cure the skin disease psoriasis appears to be particularly effective against malaria. The antimalarial properties were revealed thanks to one researcher’s inspired hunch when the psoriasis drug discovery programme came to a dead end.read more
Radboud university medical center opens first healthcare AI labs19 September 2019
These are the first two ‘labs’ in the east of the Netherlands that are part of the national Innovation Center for Artificial Intelligence and the first health labs. With these two initiatives, Radboudumc and its partners are investing heavily in the application of AI to health care.read more
Careful prescription of addictive painkillers still necessary19 September 2019
Although the use of opioid painkillers in the Netherlands has risen over the past ten years, it is nowhere near the degree to which they are used in the United States, say Arnt Schellekens and his colleagues in an article published in The Lancet Public Health.read more
Exercising at home has a positive effect on Parkinson's patients19 September 2019
In a large double-blind study, Radboudumc researchers show that patients in the early stages of Parkinson's disease can exercise regularly at home for 6 months.read more
A personal touch of Kartika Hapsari18 September 2019
In order to promote interaction amongst colleagues within RIMLS, we have a ‘personal touch’ series setting employees in the spotlight. A light-hearted manner to learn about the colleagues you know and those you don’t. This week: Kartika Hapsari.read more