NL
DE
19 February 2018
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.
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 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
Renee Salz wins prize for best presentation
10 May 2022 Renee Salz won the award for best oral presentation during the Rolduc genetics retreat, organized by the Dutch and Belgian Societies of Human Genetics in Brugge. Her presentation was titled "Variant effect prediction based on long read transcriptomes". read more
Large NWA ORC grant awarded for national skin research: Next Generation ImmunoDermatology
23 March 2022 Research for better treatment methods for chronic skin diseases. read more
Novel high-resolution targeted sequencing of the cervicovaginal microbiome published in the Journal of BMC Biology
28 December 2021 This project of William Melchers, Karolina Andralojc and Mariano Molina describe a novel sequencing method to profile the cervicovaginal microbiome at the species level and with the potential to elucidate the role of the microbiome in hrHPV-induced carcinogenesis. read more
DeepRank: a deep learning framework for data mining 3D protein-protein interfaces
8 December 2021 Li Xue and colleagues recently published ''DeepRank, a deep learning framework for data mining 3D protein-protein structures'' in Nature Communications. read more
Joining forces with patient communities to drive FAIR data
17 March 2021 Nawel van Lin created a new animation, which was presented during the event on Duchenne data sharing to spread awareness of the benefits of FAIR. read more
