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.

Using the newly obtained knowledge, we aim to implement the histopathological analysis of invertebrate samples in our lab at National Institute of Biology (NIB), in the case of hepatopancreas samples using the designed binominal scoring to describe the overall presence/absence of histological changes and ordinal method with scoring of several test fields.

The visit was funded by Instruct.SI to which Katarina Bačnik thanks for support.

Bekavac, A., Beck, A., Dragičević, P., Dragun, Z., Maguire, I., Ivanković, D., Fiket, Ž., Gračan, R., & Hudina, S. (2022). Disturbance in invasion? Idiopathic necrotizing hepatopancreatitis in the signal crayfish Pacifastacus leniusculus (Dana, 1852) in Croatia. Journal of Fish Diseases, 45(2), 261–276. https://doi.org/10.1111/jfd.13552

The workshop will focus on applying PyRosetta and AI tools like RFdiffusion or ProteinMPNN to the design and engineering of proteins. The workshop is intended for early career researchers who look to get a wide overview of modern computational design techniques, try them out and discuss their use cases, limitations, and ways to improve them. The prerequisites for the workshop are:

• Basic knowledge of python (for loops, jupyter notebook, Google Colab).
• Basic knowledge of protein structure and intermolecular interactions (h-bonds, salt bridges, secondary structure of proteins).
• You need to bring your own laptop and have a Google account.

Few more details:

• Event start: Tuesday, 14^th of October 2025, at 10:00 AM
• Event end: Saturday, 18^th of October 2025, at 1:00 PM
• Link to apply for the workshop: https://forms.gle/fMdLRzerNm8wQdJG7 (deadline: 15^th of September 2025)
• There is no registration fee!

• Expanded Instruct Centre offering: The family of Instruct centres grew by one new centre in Germany (facilities in Frankfurt, Munich, Berlin, Hamburg and Jülich), and the existing centre in Spain expanded by offering new and innovative facilities in Madrid, Bilbao and Barcelona. Find out more here.
• The European Comission recognized Instruct’s commitment to advancing gender equality and awarded it with the Newcomer Gender Equality Champion award. Find out more here.
• Latvia, an Instruct-ERIC member country, has now an Instruct-ERIC Research Site and as such provides training, outreach and networking activities for Instruct users. The Latvian site is formed by Latvian Biomedical Research and Study Centre (LBMC) and Latvian Institute of Organic Synthesis (LIOS), both in Riga. Find out more here.

More info on the event that will take place from 11^th to 14^th November 2025 at the National Institute of Chemistry, Ljubljana, is available on a dedicated workshop webpage.

• Talks by leading experts in the field
• Poster sessions
• Selected abstract talks

There are student fellowships available, and the event will also include the announcement of the prestigious Bertini Award 2026. In addition, the meeting will include Instruct-ERIC Women in Science Workshop, made possible following Instruct-ERIC recognition with the European Commission Gender Equality Prize.

Registrations are already open!

More information is available via the links:

• Announcement on the Instruct-ERIC website
• Conference website

RosettaCon brings together scientists from diverse fields—structural biology, computational modeling, bioengineering, and machine learning—to explore the latest developments in:

• Protein design with Rosetta and deep learning
• Structural modeling of proteins, protein-ligand interactions, antibodies, membrane proteins, protein-nucleic acid complexes and and all other macromolecules you like to model
• Antibody and vaccine design
• Enzyme design
• AlphaFold, ESMFold, RoseTTAFold, ProteinMPNN, language models for
• structure prediction and design
• Language models to bridge chemistry and biology
• Code development and community involvement

Whether you’re a long-time user of Rosetta, new to the field, or simply curious about the future of protein structure prediction and design, Rosetta Protein Design Conference offers a welcoming, scientifically rich environment to connect, learn, and collaborate.

Inportant links:

• Conference website, including preliminary list of speakers etc: https://europeanrosettacon.org/
• Registrations: https://pretix.eu/SBD/RCon2025/

Participants from the member institutions of the Instruct.SI consortium are eligible for the same price as Slovenian Biohemical Society (SBD) and Rosetta Commons members. Additionally, a limited number of spots are available for master’s students at a discounted price of 15 EUR. Students can use the voucher code MSCBSC during registration to access this rate.

The conference is organized with the support of Instruct.SI, Slovenian Biohemical Society (SBD), National Institute of Chemistry, and Rosetta Commons.

This 4-day intensive workshop is designed for PhD students who want to combine computational nanobody discovery with experimental panning workflows. Participants will work in small groups and engage in hands-on laboratory sessions, computational tutorials, and peer presentations.

Topics include:

• Nanobody library construction and display
• Repertoire profiling and homology modelling
• Virtual panning and docking
• Phage display selection against model antigens
• Biophysical optimisation and structural applications
• Advanced imaging and live-cell compatibility
• Daily PhD2PhD research presentation series

Info:

• Venue: University of Nova Gorica, Campus Rožna Dolina, Vipavska cesta 13, Nova Gorica, Slovenia
• Eligibility: PhD students in molecular biology, structural biology, biochemistry or related fields
• Open to international students
• Fee: 300 EUR (includes accommodation, meals, and lab materials)
• Application deadline: 3 August 2025
• More info on workshop website: https://indico.ijs.si/e/nanobody_panning

Supported by: Instruct-ERIC Slovenia, SMASH (MSCA) and the University of Nova Gorica.