Programme features

The goal of this FEBS Advanced Course is to equip participants with the practical skills to address real-world protein engineering problems using state-of-the-art computational design tools. The program is structured around three complementary components: (i) thematic lectures that introduce key challenges and emerging directions in protein design; (ii) hands-on sessions that train participants in the use of cutting-edge computational tools; and (iii) a group project where participants will plan, manage, and execute a realistic protein design task. By the end of the course, participants will not only understand current challenges in the field but also gain the confidence to apply advanced protein design strategies in their own research.

Thematic lectures

The week-long course features five 2-hour lectures:

1. Dek Woolfson and [colleague] will provide a general introduction to protein design, covering key paradigms and major breakthroughs.
2. Bruno Correia and Susana Vazquez will present the state of the art in protein–protein interaction design.
3. Ajasja Ljubetič and Alena Khmelinskaia will focus on self-assembling protein materials and molecular machines.
4. Patrick Barth and Anastassia Vorobieva will introduce the principles of membrane protein design.
5. Noelia Ferruz and Birte Höcker will discuss the design of small-molecule binders and enzymes.

Tutorials

The course also includes four hands-on tutorials, introducing the key approaches and tools used to address these challenges:

1. BindCraft and other AlphaFold2 hallucination-based methods.
2. Physics-based protein design with the Rosetta molecular modeling suite.
3. AI-enabled protein design pipelines: RFdiffusion, ProteinMPNN, and ColabFold.
4. ProtGPT and other protein language models (pLMs).

Group project

Participants will be assigned to small, diverse teams, formed based on the self-evaluation and coding assignment submitted during registration. Each group will bring together complementary expertise from both wet-lab and dry-lab backgrounds.

Teams will work on pre-defined design challenges provided by the organizers. After an introductory session and kick-off meeting on day 1, groups will have the freedom to organize their work independently. Daily tutoring sessions will be available for guidance and troubleshooting, though participation is optional, allowing teams to work where and how they prefer. On the final day, each group will present their project outcomes in short talks, followed by a collective debrief on their course experience.

Posters

On day 2, participants will present posters showcasing their own research. This session provides an opportunity to reflect on how newly acquired skills can advance their projects, while also fostering networking and discussion with peers and lecturers.