How molecules communicate

Original item by Surf (in Dutch) available here.

Molecules also communicate with each other. How they do that, is what Alexandre Bonvin, professor of computational structural biology at Utrecht University, is trying to predict. And for this he uses computer power from all over the world through the European Open Science Cloud and the European Grid Infrastructure (EGI).

Complexe calculation models

Biomolecules include proteins that communicate with each other. Complex calculation models are needed to find out how they do this. Bonvin: “A communication error of the molecules or networks of molecules is at the root of many diseases and conditions. Molecules often communicate using a shutter and lock principle. Suppose you block certain locks, you might be able to stop or slow down some diseases. Think of the coronavirus, if you can discover how the proteins in the cells of the virus bind, then you have a chance to develop a vaccine or drug. Our software can support this.”

At atomic level

The research of Bonvin and his colleagues focuses on the development of reliable bioinformatics and computational approaches for predicting, modeling and parsing biomolecular interactions at the atomic level. In ordinary human language: they are making 3D models of molecules and molecular networks. For this they developed a software called HADDOCK. Researchers can then use this software again.


Via HADDOCK, for example, research is being conducted into the spread of brain tumors in the body. Understanding the mechanism of tumor growth is important for medical treatment. Researchers at the University of Bordeaux were able to use the software to test the interaction between a molecule – involved in cancer processes – and a membrane receptor that regulates tumor enlargement.


Users upload the data via a web portal. The international grid of EGI also helps with this. “The calculations are sent out into the world,” Bonvin explains. “All over Europe, but also, for example, China, Taiwan or the US, about 25 million a year. In addition, approximately 70 percent goes via the SURF network. Calculating the models requires enormous computing power. The great advantage of this method is that the calculations do not take weeks or even months, but days. We can also continue to use our own computers to tinker with the methodology. ”

Around the world

“The great thing about my work? Our software and methodology is used by users from all over the world, in 110 different countries,” says Bonvin. “It is fantastic to see that this provides new insights. Not only researchers, but also students are increasingly finding their way to our platform. ”

Structural biology in the clouds: a 10-year-old success story

The structural biology community published an extensive presentation showcasing the successes of the 10-year-old collaboration with EGI.

The community’s MoBrain collaboration is developing online portals for life scientists worldwide and relies on High-Throughput Computing and Online Storage services provided by the EGI Federation. In total, seven EGI data centres have offered around 75 million hours of computing time and more than 50 TB storage capacity to the research collaboration.

The MoBrain portals powered by EGI resources are: HADDOCK, DisVis, AMBER, CS-Rosetta, FANTEN and PowerFit. The web portal HADDOCK, for example, has so far processed more than 198,000 submissions from over 10,000 scientists, which translates into 8 million HTC computing jobs to EGI resources per year.

More usage trends and results of the partnership are available in the presentation.

The collaboration with EGI continues at the present time with a suite of dedicated thematic services within the EOSC-hub project.