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


Extended deadlines grant proposals

31 March 2020

The deadlines to submit grant proposals has been extended by most funding agencies.

read more

HFSP Grant for Johannes Textor

30 March 2020

Johannes Textor, theme Cancer development and immune defense, has been awarded a program grant of 1 million US dollars by The Human Frontier Science Program (HFSP) to investigate how T cells navigate extremely dense environments using experiments, modeling and methods from pedestrian dynamics.

read more

Ritalin enhances your ability to do tasks by making you more motivated

26 March 2020

A new study uncovers how stimulants like Ritalin work in the brain, and it challenges some misconceptions for its recreative use. The collaboration between Radboudumc and Brown University (USA) was published in the journal Science.

read more

Dealing with COVID-19 in low- and middle-income countries

26 March 2020

RIHS researcher Joost Hopman believes that low-and middle-income countries should intensify their preparedness for a possible COVID-19 outbreak. This was the core message of an opinion article that he wrote at the request of the medical journal JAMA.

read more

Physiotherapy is important to the recovery of patients with the coronavirus

26 March 2020

Patients who have been infected with the coronavirus and admitted to the hospital for this reason should receive physiotherapy as soon as their condition allows. This is the view expressed by physiotherapists and researchers from the Radboudumc in a set of joint treatment recommendations.

read more

Healthcare utilization and regional variation of end-of-life hospital care in Dutch cancer patients

26 March 2020

In International Journal of Quality Health Care RIHS researcher Femke Atsma showed high healthcare utilization and medical variation in End of Life care in Cancer patients, which was not associated with GP care or long term care.

read more