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. ”

EGI Conference 2020 dates and venue confirmed!

We are happy to announce that we have confirmed the dates for our postponed annual conference, and we like to ask you to block the 2nd up until the 4th of November. Our usual June edition is moving to a Winter period, but we will ensure to receive you with a warm welcome at the Royal Tropical Institute in Amsterdam.

Needless to say we are carefully monitoring the developments of the covid-19 situation, health and safety always come first. Please keep an eye out on our website and other communication channels for updates.

HADDOCK Portal for COVID-19

HADDOCK (High Ambiguity Driven protein-protein DOCKing) is an integrative platform developed at Utrecht University for the modelling of biomolecular complexes. HADDOCK distinguishes itself from other docking methods in the fact that it can use a large variety of experimental and bioinformatics data to drive the docking process. HADDOCK can deal with a large class of modelling problems including protein-protein, protein-nucleic acids, protein-peptide and protein-ligand complexes.

Since 2008 HADDOCK has been offered as a web portal, freely accessible to non-profit users as part of the WeNMR services and supported by the EGI Federation to scale up the computing resources available to the its users. HADDOCK is also a thematic service in the European Open Science Cloud marketplace. This strategy has maximized the impact and valorisation of this software tool. Besides the application software, the service also provides automated pre- and post-processing, compute, temporary storage and job scheduling and monitoring for running the application, so that researchers do not need to worry about application porting and compute infrastructure. The portal is heavily used with >15500 registered users from >110 countries (see statistics).

In the context of COVID-19 related research the WeNMR portal has seen an increase of registrations over the last weeks with many users indicating they intend to use it for COVID-19 projects. HADDOCK is also a core software in the BioExcel Center of Excellence and BioExcel has also committed to support COVID-19 researchers. As such the HADDOCK WeNMR team in Utrecht is already involved in several collaborations. For this purpose, together with EGI/EOSC experts, the team is looking both into expanding the processing capacity of the HADDOCK portals and providing customized solutions to support researchers. These might take the form of dedicated virtual clusters with a HADDOCK frontend running on EGI federated cloud resources, and customized virtual machines (VMs) with ready to run local HADDOCK installation for experienced users wanting to use the software at the command line.

Read more about the EGI Covid-19 initiatives.

EGI and COVID-19

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Update 16 March 2020

Due to the spreading of the COVID-19 outbreak, the EGI Foundation is working with partners to conduct a thorough impact assessment across the EGI Federation services, the EGI Federation central services and other assets, with the purpose of putting in place contingency measures that aim at maximizing the availability of all services. We are also assessing the impact on our community events, and the EGI Conference 2020, which for the moment remains confirmed on 23-25 June 2020. More information will follow on this website in the coming weeks.

As advised by the Dutch National Institute for Public Health and the Environment all EGI Foundation employees have moved remote working until the 6th of April, therefore the office (Science Park 140, Amsterdam) is temporarily closed. Business at the EGI Foundation is expected to continue as usual, and all our staff members will be approachable via their contact details which you can find on our team page