I am very grateful for the opportunity to participate in this excellent course, which provided valuable practical experience and expanded my knowledge of biophysical characterization methods. I would highly recommend this opportunity to other researchers interested in biomolecular biophysics.

Summer school was supported by Instruct.SI.

The University of Ljubljana, Biotechnical Faculty, and Instruct.SI invite you to a hands-on workshop connecting experimental biochemistry and structural biology with modern computational methods for protein design.

• When? 17–18 December 2026
• Where? Department of Biology, Biotechnical Faculty, University of Ljubljana (Večna pot 111, Ljubljana, Slovenia)
• Until when I need to apply? Application deadline: 15 November 2026 via this online form

Through practical exercises, you will explore modern software and deep learning tools and learn how to apply them in your own research projects.

What will you learn?

• Backbone design: use diffusion models to generate new protein folds or adapt natural ones.
• Sequence design: use inverse-folding models to design sequences for new backbones or improve existing proteins.
• Screening: use structure prediction and protein language models to identify promising candidates.
• Case study: bring these approaches together.

The workshop will be led by Dr. Béla Frohn, postdoctoral researcher at the AITHYRA Institute, with guest lecturer Dr. Ajasja Ljubetič, Research Assistant Professor at the National Institute of Chemistry.

Who should apply?

Researchers at all career stages, especially young scientists, with basic knowledge of structural biology who wish to acquire or strengthen practical skills in computational protein design.

Participation is limited to 20 attendees, selected based on their CV and motivation letter.

Submit your CV and motivation letter by 15 November 2026: Apply here!

All details can to be found on the workshop website

All details are to be found in the attached PDF invitation and at the dedicated subpage SPA2026.

• Workshop: De Novo Protein Design for Beginners (Linking Artificial Intelligence and Experimental Biochemistry), tentatively in September 2026 (University of Ljubljana, Biotechnical Faculty)
• Workshop: Introduction to Phage Display Technology and Computational Methods for the Isolation of Binding Proteins, 23–25 September 2026 (University of Nova Gorica)
• Workshop: Cryo-EM Workshop, Single Particle Analysis, 10–12 November 2026 (National Institute of Chemistry)
• Workshop: Biophysical Characterization of Proteins, 2–3 December 2026 (University of Ljubljana, Faculty of Chemistry and Chemical Technology)
• Symposium: One-day scientific symposium, at National Institute of Chemistry, 18 November 2026 (Instruct.SI members)

Please follow our announcements on this website and other channels (e.g., mailing list of Slovenian Biochemical Society) for additional information.

This collaboration aimed to elucidate the structural basis for the relationship link between increased iodination of thyroglobulin (TG) and its potential link to autoimmunity and thyroid disorders. During his visit he used protein production and EM facility available at Human Technopol Institute. Negative-stain electron microscopy was performed on iodinated TG samples to assess structural characteristics and sample quality for further structural studies. Recombinant iodine-free TG produced during the visit was used for time-resolved LC-MS/MS analysis of iodination. This revealed more iodination sites than expected and suggests a sequential nature of iodination in which hormonogenic sites may be modified earlier, indicating a potentially more focused repertoire of iodinated autoimmunogenic epitopes.

This visit contributed to the transfer of advanced methodology and the expansion of structural expertise in Slovenia.

The visit was funded by Instruct.SI to which they thank for support.

New Instruments

• Protein production: two shaker incubators and a chromatography system for preparation and purification of recombinant proteins (National Institute of Chemistry, Department of Molecular Biology and Nanobiotechnology)
• Protein quality control etc: instrument for characterization of protein conformational and colloidal stability NanoTemper Prometheus Panta (University of Ljubljana, Faculty of Chemistry and Chemical Technology, Chair of Biochemistry)
• Molecular interactions: surface plasmon resonance (SPR) instrument for label-free real-time molecular interaction analysis, Cytiva Biacore 1S+ (University of Ljubljana, Biotechnical Faculty, Department of Biology)
• Macromolecular characterization: Raman spectrometer coupled with atomic force microscopy (AFM) (University of Ljubljana, Biotechnical Faculty, Department of Food Science and Technology, Chair of Biochemistry and Food Chemistry)

Meetings and outreach

• Nanobodies Workshop: Binder Recovery by In Silico and In Vitro Panning, September 22–26, 2025 (University of Nova Gorica), combining computational nanobody discovery with experimental panning workflows
• Rosetta Workshop, October 14–18, 2025 (National Institute of Chemistry), focused on applying PyRosetta and AI tools (RFdiffusion, ProteinMPNN) in protein design, followed by the 4^th EU Rosetta Protein Design Conference, Ljubljana, October 20–22, 2025
• Instruct.SI Cryo-EM Advanced Workshop on Single Particle Analysis, November 11–14, 2025 (National Institute of Chemistry), covering SPA workflow: grid preparation, data collection and data analysis
• Lectures of Peter Podbevšek and Nika Žibrat (National Institute of Chemistry), at the Instruct-ERIC Webinar Series Structure Meets Function, June 17, 2025
• Cryo-EM facility at the National Institute of Chemistry hosted >90 external visitors
• Workshop on Structural Biology and Physiology, September 26, 2025, and Regional Physiology Meeting, September 24–27, 2025, Ljubljana

Building on these achievements, Instruct.SI enters the coming year well positioned to further strengthen research infrastructure, expertise, and collaboration in integrative structural biology.

A key feature of this year’s workshop was the opportunity for participants to bring their own research samples. Four attendees took advantage of this, and all participants prepared multiple cryoEM grids during the practical sessions. Under close mentorship from several tutors, they successfully vitrified their samples, gained confidence in handling the Vitrobot IV, and developed a strong understanding of best practices for grid preparation. The small-group format allowed for individualised guidance and ensured that everyone produced usable grids and learned from real experimental outcomes. Beyond sample preparation, the workshop also emphasised microscope operation, screening strategies, and data collection. Participants worked with the 200 kV Glacios cryoTEM, learning step by step from how to load grids to setting up data collection.

The final part of the programme focused on data processing and 3D reconstruction, giving participants a complete overview of the single particle analysis pipeline – from motion correction and CTF estimation to particle picking, 2D classification, and initial 3D refinement. Guided sessions supported by five tutors enabled each participant to follow the process on a real dataset and understand how individual steps influence the final result.

Overall, the workshop offered a concentrated and highly practical experience, allowing participants not only to observe but also to actively perform each stage of the workflow. The positive feedback we received underscores the value of small, skill-focused workshops within the Instruct.SI community. Building on this success, we aim to continue offering advanced, practice-oriented training opportunities to support researchers in Slovenia as they further develop expertise in cryo-electron microscopy.

More photos are available in the gallery.

This collaborative research aimed to gain a better understanding of viral cellular infection mechanisms through innovative protein inhibitor design and high-resolution microscopy. At the Jožef Stefan Institute, novel protein inhibitors targeting proteases involved in viral cell entry have been developed. These inhibitors are designed to localize in specific intracellular compartments such as lysosomes, endosomes, and the endoplasmic reticulum. Their expression has been verified through several experimental methods. During her visit she used advanced confocal microscopy and image analysis tools available at Constructor University to map and quantify the subcellular distribution of these inhibitors. By combining high-resolution microscopy with knowledge of structural biology, they have developed methods for visualizing how inhibitors and proteases interact with each other and how they are organized within cells. The visit also contributed to the transfer of advanced microscopy methodologies and the expansion of structural biology expertise in Slovenia.

The visit was funded by Instruct.SI to which they thank for support.