19 February 2018

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


The Postdoctoral Networking Tour in artificial intelligence

2 July 2020

You are a postdoctoral researcher in the field of artificial intelligence? The Postdoc-NeT-AI offers you the opportunity to participate in one week of on-site visits to leading German universities, research institutes and companies. Apply now to this year's tour until 16 August 2020.

read more

Register for Phd courses via gROW What does this mean for you?

2 July 2020

From now on you can arrange everything related to the general RU PhD courses via gROW. Because of this there will be some changes in the registration! What does this mean for you?

read more

Experts on metabolic diseases still an unknown major problem...

1 July 2020

Six Dutch UMCs and a patient association contribute to treating and solving this major, often unknown, problem. Timely detection of metabolic diseases is vital. Therefore, Radboudumc is also part of the consortium “United for Metabolic Diseases”.

read more

Radboud Pluim for Lionne Ekers ambassador for the RIMLS institute

30 June 2020

Lionne Ekers received the Radboudpluim for her special merits for the Radboudumc. She is a born ambassador for our Institute.

read more

Stefan Listl member Lancet Commission on Oral Health

29 June 2020

In recognition of the global public health importance, woeful neglect of oral diseases, and the need for a broader understanding and commitment to global oral health within medicine and global health agendas, The Lancet recently established a Commission on Oral Health.

read more

Trained immunity: a tool for reducing susceptibility to and the severity of SARS-CoV-2 infection

29 June 2020

In a review in Cell Mihai Netea, Frank van de Veerdonk, Reinout van Crevel and Jorge Dominguez Andres propose that induction of trained immunity by whole-microorganism vaccines may represent an important tool for reducing susceptibility to and severity of SARS-CoV-2.

read more