By Richard Norman and Atte Sillanpää
Since we launched our first BioExcel Summer School on Biomolecular Simulations in 2018, this yearly event has allowed Ph.D. and post-doc researchers to come together in a relaxed and friendly environment to engage in training and face-to-face conversations with internationally recognised leaders and code developers in the field of computational biomolecular research. This year our Summer School was no different;
The school was held over a period of 5 days at the beautiful Sardegna Ricerche by the beach in Pula, Sardinia and had 30 participants and 13 lecturers and trainers from across Europe taking part. It witnessed the coming together of participants, full of enthusiasm and open minds to gain knowledge and new skills, discuss and share their personal experiences, thus making for a memorable event of learning and community building.
Day 1 featured two of BioExcel’s core codes, GROMACS and BioExcel Building Blocks (BioBB). Alessandra Villa from KTH Royal Institute of Technology gave an introduction to Molecular Dynamics and the use of GROMACS, and highlighted the importance we place on gathering user feedback to drive software development. Adam Hospital from IRB Barcelona introduced the much improved BioExcel Building Blocks (BioBB) software library. A collection of BioBB modules (categories) exist to help users perform biomolecular simulations reproducibly. You can learn more about it from the official BioExcel BioBB webpage.
Day 2 celebrated 20 years of integrative modeling with another BioExcel’s core code: HADDOCK. Marco Giulini and Rodrigo Vargas Honorato from Utrecht University discussed how AI, antibodies and small molecules can come together in the new modular version of the software: HADDOCK3. This was followed by a hands-on session where participants were able to put theory into practice through some of the tutorials which can also be accessed from the official BioExcel HADDOCK webpage.
Day 3 was all about enhanced sampling and the following quote summarizes its importance: “supercomputers are faster than ever, but it’s the enhanced sampling techniques that will really give you speed and efficiency in MD simulations.” The official GROMACS tutorials webpage has a number of tutorials on enhanced sampling methods and Erik Lindahl introduced participants to the tools available and things to remember before running biomolecular simulations. These guidelines gathered much interest on social media and a number of individuals wished they had access to these words of wisdom when starting out in the field. We are working to produce a perhaps more complete version and will publish this in future.
Also on day 3, Attilio Vittorio Vargiu and Giuliano Malloci showcased some enhanced sampling techniques applied to molecular recognition via multiple use cases. The tutorial on the EDES method used during the hands-on session can be accessed through the official Università degli Studi di Cagliari Molecular Modeling Lab webpage. Attilio and Giuliano are also our local collaborators and play a key role to ensure the event runs smoothly overall. Starting from the initial planning and enabling the software installations on the local laptops to welcoming us at the airport and sharing their local knowledge. Their contributions throughout the event were essential in adapting to unforeseen issues and last minute changes, and generally anything to do with overcoming the language barrier with the locals.
During day 4, Bert de Groot from the Computational Biomolecular Dynamics group (Max Planck Society) engaged participants on the capabilities of non-equilibrium alchemy in protein engineering and drug discovery using GROMACS-pmx. Emiliano Ippoliti from Forschungszentrum Jülich talked about hybrid QM/MM approaches and applications. A hands-on session on calculating free energies to reduce the theory to practice was held in the afternoon. From the official BioExcel pmx webpage you can access the tutorial used during this session.
Day 5 and last day of the Summer School started with Jon Paul Janet from AstraZeneca giving an overview of how molecular simulations and AI are used in the pharmaceutical industry to accelerate drug design. In addition to this being a concrete example on usage of these methods, covered by BioExcel at large, it provided an example of a career in industry. This theme was continued as a separate career session presenting different career trajectories of four BioExcel members. The three best poster prize winners were also announced.
It was not all work and no play, with excursions to nearby Pula and Nora, together with some unofficial sands-on activities which helped:
Participants provided much positive feedback and if the below testimonials are anything to go by we will surely be organizing our next Summer School along the same lines and looking forward to welcoming a new group of enthusiastic students in June 2024!
“In conclusion, the quality of teaching, the ratio of breaks/lectures, and the overall vibes made this summer school a life experience that I would forever cherish and recommend anyone to participate in.”
“The lectures were excellent in content and also the course was structured with a proper timing in between lectures, breaks and tutorials. The structure of the course was perfect and I learn and enjoy everything about this school.”
“The willingness of organizers and trainers to help and discuss many kinds of subjects. Having close interaction with colleagues at different levels of expertise and different backgrounds. Having and promoting a nice and healthy way of community.”
“First of all, thank you to the organizers for doing such excellent work on this summer school. The activities were really well organized, and I also liked the flexibility and adaptability of the organizers as we changed a few things on the way, but everything worked out smoothly in the end. The whatsapp group is a nice way to keep in touch with the community. For me it was an amazing experience that I can’t recommend enough to all the people in the research field. I made a lot of great connections and even friends and we already planned to meet again next year of sooner for a bioexel summer school reunion, we will see how that turns out”
