Explore the 20-year journey of HADDOCK, an integrating modelling platform shaping biomolecular research globally

By Alexandre M. M. J. Bonvin

Reflecting on two decades of evolution, the HADDOCK (High Ambiguity Driven protein-protein DOCKing) integrative platform stands as a nuanced testament to the intricate landscape of biomolecular modelling. Developed at Utrecht University, this platform has quietly and steadily contributed to the understanding of biomolecular complexes. With its roots in pioneering research, HADDOCK has played and is still playing a crucial role in shaping the field of (computational) structural biology.

The 20 year anniversary symposium held in Huizen, Netherlands, on 7-10 November 2023, marked not just a celebration of achievements, but also an opportunity to delve into the platform’s ongoing significance since the publication of the first JACS paper in 2003.

HADDOCK in support of research and education

Since the original publication in 2003, HADDOCK has constantly evolved to provide support for different information sources and molecule types, from proteins, peptides, nucleic acids, to glycans and small ligands, being easily accessible for non-profit as a web service. This web service, developed at Utrecht University and in operation since 2008, has been making use of the EGI federation HTC resources since 2010. Boasting over 41,000 registered users from more than 142 countries, the web interface provides not only graphical access to research software but also input validation, automated pre- and post-processing, compute resources, temporary storage, job scheduling and monitoring and sharing.

The original publications describing the various versions of HADDOCK and its web server have been cited more than 7000 times to date, reflecting its worldwide impact. Over the past 20 years we have also observed its embedding in educational programmes, seeing cohorts of students from various universities registering at given times throughout the year.

Currently, under BioExcel and in collaboration with the Netherlands e-Science Center, HADDOCK is now evolving toward its third major version. This new modular and flexible implementation (HADDOCK3) allows the creation of custom workflows, opening new opportunities for new scenarios and applications. This version, for which a web application is currently under development in collaboration with the Netherlands e-Science Center, is evolving from using the EGI HTC resources to use both HPC resources under EuroHPC and more cloud-based resources under EGI/EOSC.

Read also the related news article on the EGI website.