SulkowskaLab - Interdisciplinary Laboratory of Biological Systems Modelling

03/08/2026

Sun’s out, science is in! ☀️🧪

Meet the (almost) complete summer crew of the wet lab: undergrads, grad students, postdocs, and our PI all in one frame. It takes a big team to push all our projects forward, and we couldn't ask for a better group this season 🙌

15/05/2026

Big news from the lab! 📢

Our latest publication, "Knot or not? Identifying unknotted proteins in knotted families with sequence-based Machine Learning," is officially a hit! 💥 It has reached the top 10% of most-viewed papers in Protein Science for 2024. 📈

Read the popular paper (link in the comments):
Sikora M, Klimentova E, Uchal D, Sramkova D, Perlinska AP, Nguyen ML, Korpacz M, Malinowska R, Nowakowski S, Rubach P, Simecek P, Sulkowska JI. Knot or not? Identifying unknotted proteins in knotted families with sequence-based Machine Learning model. Protein Sci. 2024 Jul;33(7):e4998. doi: 10.1002/pro.4998. PMID: 38888487; PMCID: PMC11184937.

30/04/2026

💥 We are delighted to announce that our work, “Novel Knotted Solenoid fold with order-shifted coil arrangement leads to nontrivial 31 topology” has been published in the Proceedings of the National Academy of Sciences (PNAS)! 🥳🤩

This study reports a previously unknown protein architecture within solenoid folds — the Knotted Solenoids, featuring a trefoil knot (3_1) formed via a distinctive “skip-and-backtrack”🔁 mechanism. This result highlights the growing power of artificial intelligence 🧠 not only to predict structures, but also to reveal entirely new biological principles.

The work was carried out in collaboration with Prof. Sophie Jackson (University of Cambridge) and the Department of Biophysics, University of Warsaw, bringing together complementary expertise in protein folding, stability, and computational modeling 🧪🖥️

Read the full article here: https://www.pnas.org/doi/abs/10.1073/pnas.2525920123

23/03/2026

Our PhD student, Julia Sikorska, just returned from an intensive workshop focused on Protein Quality Control organised by EMBL Events in Heidelberg. Out of many applicants, she was one of only 20 researchers selected to get hands-on with the latest methods for monitoring proteins' stability and folding 👏🧪 We can’t wait to see how these new insights and techniques will push our research on knotted proteins even further!

A huge thank you to all participants, trainers, and organisers of the EMBL Course 'Protein quality control for downstream processes' 🙌

During the course, specialists from both academia and industry worked together to introduce technologies frequently used in protein quality control. The participants of learned how to use various biophysical techniques used for protein characterisation, such as SEC-MALS, DLS, SLS, mass photometry, DSF, flow induced dispersion analysis and spectroscopy.

A special thanks to our Scientific organisers:
• Karine Lapouge, EMBL Heidelberg, Germany
• Bertrand Raynal, Institut Pasteur, France
• Kim Remans, EMBL Heidelberg, Germany

And to our Conference and scientifc organisers:
• Lucia Minutta, EMBL Heidelberg, Germany
• Michelle Steinhauer, EMBL Heidelberg, Germany

See you at another one of our events soon! ➡️ https://www.embl.org/events/

23/02/2026

🚀 Research Internship & PhD Scholarship: apply now!

Join our laboratory at CeNT UW to work on the OPUS 28 Grant (2024/55/B/NZ1/03184). We are looking for ambitious Students and PhD Candidates with experimental and/or theoretical background in biology/chemistry/physics/bioinformatics to pioneer the design of non-trivial coiled-coil and alpha/beta protein folds that self-assemble both in silico and in vitro.

What’s in it for you?
🧫 Scholarship: A basic doctoral scholarship of: 6742 (4242 - doctoral scholarship paid by the Doctoral School + 2500 - by OPUS 28 NCN) PLN/month gross for the first 24 months and 8340,90 (5340,90 + 3000 respectively as above) PLN/month gross for the remaining 24 months.
🧫 Top-tier Mentoring: Work with Prof. Joanna Sułkowska, recognized among the top 2% of scientists globally.
🧫 Flexibility & Growth: Tailored working hours, conference travel, and international collaborations.

Apply now!
Send all the required documents (incl. CV, current transcript, and a brief cover letter) to Prof. Joanna Sułkowska ([email protected]). Details about the application may be found at CeNT UW website: https://cent.uw.edu.pl/pl/oferty-pracy/

17/02/2026

Czy jest połączenie między fizyką kwantową a białkami o nietrywialnej topologii .... 17 lutego Radio dla Ciebie godzina 20 z minutami

17/02/2026

‼️Student Assistant Position 👩‍🎓🧑‍🔬

⛔️ Edit: The call is closed, and no further applications can be considered.

We are looking for motivated students (biology, chemistry, or physics fields) interested in experimental or computational research 🔬🖥️

What you will do:
🧪 Assist in enzyme and protein design using machine‑learning tools.
🧪 Perform experimental validation of protein structure and function.

Who we seek:
Students with initiative, curiosity, and motivation, no prior experience required, but good to have. You may also pursue your own research topic.

What we offer:
🟢Scholarship: 1,000–1,500 PLN/month (depending on availability and experience).
🟢Flexible schedule and possibility to integrate with thesis work.
🟢Mentoring and training in AI‑based design and advanced biochemical methods.
🟢Opportunities for development, including visits to collaborators and conference participation.

To apply, send your CV, transcript of grades, and a short motivation letter to Dr. Fernando Bruno da Silva at [email protected].

14/02/2026

🔬🦠🕹️This is the first grant of this type awarded in Poland.
We received a collaboration grant from the 𝐔.𝐒. 𝐍𝐚𝐭𝐢𝐨𝐧𝐚𝐥 𝐒𝐜𝐢𝐞𝐧𝐜𝐞 𝐅𝐨𝐮𝐧𝐝𝐚𝐭𝐢𝐨𝐧 𝐍𝐚𝐭𝐢𝐨𝐧𝐚𝐥 𝐒𝐲𝐧𝐭𝐡𝐞𝐬𝐢𝐬 𝐂𝐞𝐧𝐭𝐞𝐫 𝐟𝐨𝐫 𝐄𝐦𝐞𝐫𝐠𝐞𝐧𝐜𝐞 𝐢𝐧 𝐭𝐡𝐞 𝐌𝐨𝐥𝐞𝐜𝐮𝐥𝐚𝐫 𝐚𝐧𝐝 𝐂𝐞𝐥𝐥𝐮𝐥𝐚𝐫 𝐒𝐜𝐢𝐞𝐧𝐜𝐞𝐬 (𝐍𝐂𝐄𝐌𝐒)
to conduct research in multidisciplinary scientific teams 🇦🇺🇮🇹🇬🇧 that leverage AI and data science to integrate vast publicly available datasets and address fundamental questions in molecular and cellular biology. The project aims to stimulate new research directions, resolve long-standing challenges, attract top talent, and train the next generation of data-savvy scientists while adhering to the highest standards of scientific practice.
The project will be led by 𝐉𝐨𝐚𝐧𝐧𝐚 𝐒𝐮𝐥𝐤𝐨𝐰𝐬𝐤𝐚, with student researchers Julia Sikorska and Fortunka participating in the team.

We will focus on: Unraveling the Evolutionary Origin of Complex Topologies
Centrum Nowych Technologii Uniwersytetu Warszawskiego

26/11/2025

Serdecznie zapraszamy na wykład z serii "Zapytaj fizyka", który poprowadzi prof. Sophie Jackson z Uniwersytetu w Cambridge! 🧪Prof. Jackson przybliży różne aspekty świata białek zawęźlonych - temat bardzo bliski naszej grupie... A już w piątek o godz. 12:00 w Centrum Nowych Technologii Uniwersytetu Warszawskiego prof. Jackson opowie o terapeutycznych peptydach! 🩺

🧡Zapraszamy na kolejny wykład z serii „Zapytaj fizyka”. Wykład zatytułowany: „A very knotty problem" odbędzie się we czwartek 27 listopada o godz. 18:00 w sali 0.03 na Wydziale Fizyki UW, ul. Pasteura 5. Prelegentką będzie prof. Sophie Jackson.
Prof. Sophie Jackson pracuje na Wydziale Chemii Uniwersytetu w Cambridge od 1995 r. Z tym uniwersytetem związana jest od czasu studiów doktoranckich, które odbywała także we współpracy z Imperial College. Po uzyskaniu doktoratu w 1991 r. odbyła staż podoktorski na uniwersytecie Harvarda. Prof. Jackson jest też członkinią Royal Society of Chemistry, Cambridge Philosophical Society, Biochemical Society, wielu paneli eksperckich i zespołów doradczych.
Grupa prof. Jackson zajmuje się różnymi aspektami biologicznej samo-organizacji peptydów i białek, ich strukturą, stabilnością oraz procesami zwijania. Wraz ze swoją grupą podjęła pionierskie badania nad właściwościami i ścieżkami zwijania białek zapętlonych, wykorzystując szeroki wachlarz technik eksperymentalnych. Ponadto opracowała nowatorskie metody badania potranslacyjnego zwijania takich białek i wpływu białek opiekuńczych na ten proces, wykorzystując wiele najnowocześniejszych metod biofizycznych, m.in. spektrometrię mas i szczypce optyczne.

Ogłoszenie o wykładzie:
https://zapytajfizyka.fuw.edu.pl/wyklady/sophie-jackson/