This Summer School is open to Master and PhD students with a basic background in biochemistry, structural biology, molecular biology or related fields. It's ideal for who is ready to integrate nanobody discovery into their work—computationally, experimentally or both. We will select max 10 participants based on their submitted abstract and motivation letter. Successful applicants will be notified and asked to pay a €70 registration fee (see FAQ for what is included).
🔬 What You'll Learn
How nanobody libraries are constructed, characterized, and screened
How wet-lab nanobody phage display screening of target antigen works
How computational and AI workflows are useful to store, model, rank, design and simulate nanobody candidates
🧠 Present Your Research
Each registered participant presents either their current PhD project as it relates to
nanobody research or a method/idea they plan to adopt. Talks are strictly 10 minutes, followed by a moderated
discussion with peers and lecturers. Participation in these sessions is a requirement of registration.
🤝 Collaboration & Networking
The program includes informal discussion rounds, dedicated networking events, and
social activities designed to foster connections and future collaborations.
ℹThe final Summer School programme will be available for download. Please note that changes may still occur.
Welcome & Introduction on Nanobody technology
👤 Prof. Ario de Marco (University of Nova Gorica)
🕒 Wed 23/09, 10:00
Opening Lecture
This introductory session provides a foundational overview of nanobody (VHH) libraries and their role in binder discovery. Participants will learn the key differences between immune libraries (from antigen-immunized animals), naïve or pre-immune libraries (from non-immunized sources), and synthetic libraries (constructed through targeted sequence design and CDR randomization). The session explores how library diversity is generated—through methods such as PCR amplification of VHH genes or synthetic variation—and how it influences library quality and downstream success. Common library sizes are discussed, as well as how different display platforms (e.g. phage, yeast, ribosome) are used to present libraries to antigens, with an emphasis on phage display.
🔒 Material locked (Registration required)
Nanobody in silico Screening from Pre-Immune Libraries
👤 Dr. Klara Kropivsek (University of Nova Gorica)
🕒 Wed 23/09, 11:00
Lecture & Hands-on
Recent advances in high-throughput sequencing and structure prediction have enabled “virtual panning” of naïve nanobody (VHH) repertoires. This session reviews the core modules of computational nanobody discovery: repertoire profiling via MiXCR and clonotype clustering, homology modeling with NanobodyBuilder2 and ColabFold/Boltz-2, and docking benchmarking of published VHH–antigen complexes using ZDock and Boltz-2, scored by different scoring strategies. We’ll showcase case studies from ongoing work—including clonotype analysis of a naïve llama library and redocking of SAbDab-derived VHH–antigen pairs to assess predictive performance.
🔒 Material locked (Registration required)
Nanobody de novo design with AI
👤 Dr. Marco Orlando (University of Nova Gorica)
🕒 Wed 23/09, 13:30
Lecture & Hands-on
Nanobodies (Nbs) from pre-immune libraries could exhibit deficiencies in biophysical properties, such as stability and affinity, necessitating an optimization step. This can be achieved either in vitro through controlled mutagenesis followed by another round of panning or in silico by proposing variants. This approach, which involves screening multiple single-site variants, may demand extensive experimental efforts. Additionally, negative epistatic effects can occur when combining multiple potentially beneficial single-site variants, where increased affinity variants may negatively impact stability. Emerging data-driven Machine Learning (ML) approaches are promising in the field of de novo Nb design or redesign, as they can learn multidimensional constraints between protein structure, stability and binding capacity, while explicitly designing protein and non-protein biomolecules at atomic-level resolution. Anyway, a small amount of data is available for training Nbs-specific methods and available models have been tested and validated mainly in the design of mini-binders of known protein biomarkers. In this workshop session an introduction to these methods and their expected accuracy on published data will be provided, with the possibility to try a couple of them through a Jupiter Notebook run over the internet browser in a simple case study. In the second part there will be a perspective and discussion on adapting such de novo protein design systems for nanobody CDRs (re)design tasks.
🔒 Material locked (Registration required)
Nanobody Panning Against a Target Antigen
👤 Dr. Claudia d'Ercole (University of Nova Gorica)
🕒 Wed 23/09, 15:30
Practical Briefing
In the practical part of the workshop, participants will gain hands-on experience with phage display-based nanobody panning. Working in small groups, they will perform a selection round using a nanobody (VHH) library and a chosen model antigen immobilized on a solid surface. The goal is to enrich for nanobody clones that specifically bind the target. The workflow includes incubation of the library with the antigen, washing to remove non-binders, elution of bound phages, and infection of E. coli for amplification. If time allows, participants will also explore panning on live cells to simulate more complex and physiologically relevant selection environments. Takeaway: Participants will understand and carry out the core steps of a nanobody selection campaign, gaining insight into the practical considerations and challenges of identifying specific binders from a large pre-immune or synthetic library.
🔒 Material locked (Registration required)
Molecular dynamics based evolution of epitope specific nanobodies
👤 Assistant Prof. Sara Fortuna (Dipartimento di Scienze Matematiche, Informatiche e Fisiche, Università di Udine)
🕒 Fri 25/09, 09:00
Special Lecture
Molecular modelling allows addressing an important bottleneck of antibodies engineering: the control over their target binding site. To reach this goal we have developed an improved parallelised evolutionary algorithm for the computational optimization of generic aminoacid based binders. The code, through a combination of molecular dynamics simulation and free energy estimations, allows to iteratively improve epoch by epoch the predicted binding affinity of a pool of binders. Our result shows the obtained nanobodies capable of captutring the target through the pre-chosen binding site. This holds true even when no prior experimental data is available.
🔒 Material locked (Registration required)
Data Quality Challenges and Structural Artifacts in Nanobody–Antigen Databases
After registration, you will receive instructions on how to submit an abstract.
Please get in contact for any need of info and indications about how to reach the campus, even prior to proceed with registration. The registration can be cancelled with 100% refund if done by 1st September 2026. No refund is available for later cancellation.
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We'll share a full schedule soon, but you can already look forward to relaxed after-hours gatherings designed to bring everyone together. We will have a social dinner with all the speakers on the second day. The Summer School overlaps with "Gusti di Frontiera", the most awaited event of the year for the city of Gorizia: as every year, along the main city streets several food and beverage enogastronomic stands will arrive from all over the world, and will be accompanied with music, fun and shows. An event to not miss!
No. Selected participants pay a €70 registration fee, which covers:
Accommodation at Šempeter (see Q2)
All meals (lunches, coffee breaks) and social events
Wet-lab consumables and materials
Transport costs we organize during the Summer School are covered. Transport costs to reach the campus from your place are not covered.
2. What accommodation is provided?
We provide free accommodation near the campus from 22nd to 26th September. We've reserved rooms at Šempeter, immersed in the green and 30 min by foot distance to the campus and to the Gusti di Frontiera event. Public transport is free during Summer School attendance.
3. Can I earn ECTS credits?
We do not directly award ECTS credits. However, we will issue an official Certificate of Attendance
indicating the Summer School's workload and learning outcomes.
4. Is the Summer School open to international applicants?
Yes, researchers from any country are welcome to apply. We're happy to provide invitation letters and
supporting documents to help with your visa application.
5. What food will be served?
We cater to all dietary needs—vegetarian, vegan, gluten-free, halal, etc. When you register, you'll be asked
to specify any dietary restrictions or allergies.
8. What is the cancellation policy?
Free cancellation up to 1.9.2026. No refunds for cancellations made after 1.9.2026.
About the Organisers
This Summer School is jointly organised by members of the Laboratory of Environmental and Life Sciences at the University of Nova Gorica. We are grateful for the support of everyone who helped to make this event possible.
Organising Committee
Dr. Marco Orlando, Dr. Klara Kropivšek, Prof. Ario de Marco, Dr. Claudia D'Ercole, Prof. Iain R. White, Nadja Lovec Santinello
About the Research
The Ario de Marco group specialises in scalable nanobody production, focusing on
efficient microbial expression systems and robust purification protocols. They have developed and refined
phage display selection strategies to isolate high-affinity binders, often integrating deep sequencing to
monitor selection dynamics and improve target coverage.
We'll share a full schedule soon, but you can already look forward to relaxed after-hours gatherings designed to bring everyone together. We will have a social dinner with all the speakers on the second day. The Summer School overlaps with "Gusti di Frontiera", the most awaited event of the year for the city of Gorizia: as every year, along the main city streets several food and beverage enogastronomic stands will arrive from all over the world, and will be accompanied with music, fun and shows. An event to not miss!
Source: Il Piccolo