By Atte Sillanpää and Richard Norman
Our flagship training event is now in its 8th year and was held in Pula, Sardinia, during the second week of June. As with previous years, the school was heavily overbooked and participant selection was based on experience and career stage but also to maximise participation from different European countries. Indeed, we had participants from 11 countries representing 16 nationalities with an almost 50:50 gender ratio and, importantly, with diverse competences, interests and backgrounds within the scope of the school.
The school covered all of the BioExcel core applications and more; the program consists of lectures and related hands-on exercises which help to consolidate the theory and ensure participants can start applying their new found skills on their own research problems.
The first day was all about Molecular Dynamics with Prof. Berk Hess and Cathrine Bergh providing a nice introduction to the topic and the use of GROMACS, reminding participants that for a while now there is an expectation that experimental results are supported by simulations when publishing in scientific journals. You can find the “Introduction to Molecular Dynamics” tutorial which was used through the GROMACS tutorials page.
Molecular recognition and docking were the topics for day two with Prof. Alexandre Bonvin introducing the use of HADDOCK to predict interactions between a plethora of distinct molecular types including proteins, nucleic acids, glycans and small molecules. The new modular version of HADDOCK (HADDOCK3) allows for further flexibility and customisation of tasks. Anna Kravchenko took participants through the HADDOCK3 tutorial for antibody-antigen modeling. Attilio Vittorio Vargiu gave an in-depth brainstorming lecture on biomolecular recognition and enhanced sampling methods, covering techniques like Replica Exchange MD, Metadynamics, Accelerated MD, Targeted MD, and more, illustrated with multiple case studies. This was followed by a tutorial which enabled participants to test the EDES method for enhanced sampling.
Enhanced sampling and free energy calculations were the main topics covered on day three. Berk Hess introduced the accelerated weight histogram (AWH) method implemented in GROMACS and illustrated its application to alchemical transformations where the main challenge is to define a good reaction coordinate. This was illustrated during the hands-on session on calculating the potential of mean force (PMF) along a reaction coordinate using the AWH method in GROMACS. We also have a webinar on its application. Sudarshan Behera gave an introduction to free energy calculations followed by a tutorial on using PMX and GROMACS to set up a ligand-binding relative free energy calculation study, and we also have a webinar on this.
Berk Hess talks about the AWH method.
On day four, Adam Hospital introduced BioExcel Building Blocks (BioBB) and followed up with a hands-on tutorial on how to use BioBB to perform protein-ligand complex Molecular Dynamics using GROMACS in Jupyter notebooks. During the afternoon, and in response to community feedback, we were joined online by Sergey Ovchinnikov from MIT who gave participants some invaluable insights into Alphafold. Sergey talked about AlphaFold3 and its limitations, and if you are looking for alternatives, check out ColabFold.
On the last day of the school we finished off with an introduction to QM/MM by Emiliano Ippoliti and as part of our commitment to career development we held a session for all participants with representatives from industry and academia. Joining Alexandre Bonvin and Berk Hess were Alexis Molina from Nostrum Biodiscovery and our BioExcel Ambassador for Norway Nathalie Reuter from University of Bergen. Participants prepared around 20 questions for the panel which covered a range of topics from deciding between a career in academia or industry, which soft skills are most important, how to achieve a work-life balance, to optimizing a CV for job interviews.
The school is as much about learning and implementing the core software as it is about engaging with and making connections with the lecturers, code developers and other researchers in the community. To this end, the introductory participant flash-talks on day one, dedicated poster sessions and informal environment around meals and down-time created a relaxed environment which lowers to interaction and knowledge exchange.
Get an impression of what its like at the Summer School and hear one of this year’s participants, Federico Natale, describe his expectations and the value which the Summer School has brough for him to date.
Following last year’s success, we again asked the participants to vote for the best poster, with almost all received votes. The three winners will get to present their work in a special edition of the BioExcel webinar series on the 23rd of September.
Poster prize winners (clockwise from top left): Zuzana Janáčková, Gesa Laura Freimann and Jan van Elteren.
This year’s participants scored the school 9.1/10 with some of the reasons for the high rating being based on the following feedback:
“Listening to the foremost experts in this field and having the ability to ask about anything is invaluable.”
“I liked the guided hands-on sessions more than the completely free sessions.”
“Rated based on the quality of the explanation, way of discussing questions and curiosity, as well as the give the chance to think and be creative in the tutorial.”
“The sessions were organized well. Differences originated mostly between the different styles of teaching/presenting of the respective presenters.”
“Workshops with quick follow-along first and independent exercise then later were best for learning. Exercises where you don’t just follow theory and lines of codes, but instead are given a task to complete and figure for yourself with online resources + personal assistance really helped following along.”
And in response to the question “What was the best part of the School?” the top answers were related to networking with other participants and the lecturers, and the overall quality of the lectures and tutorials.
As with previous years, the Summer School was a great success and we look forward to next years event in June 2026.
