Publications

Full list of publications can be found here.

Featured publications

* ... shared first author
✉ ... shared corresponding/senior author

Massively parallel measurement of protein–protein interactions by sequencing using MP3‑seq
A Baryshev*, A La Fleur*, B Groves, C Michel, D Baker, A Ljubetič✉, G Seelig✉
Nature chemical biology, August 2024 (Read more)

A multiplexed bacterial two‑hybrid for rapid characterization of protein–protein interactions and iterative protein design
WC Boldridge*, A Ljubetič*✉, H Kim, N Lubock, D Szilágyi, J Lee, A Brodnik, J Jerala✉, S Kosuri✉
Nature Communications, August 2023 (Read more)

Design of in vivo self‑assembling coiled‑coil protein origami
A Ljubetič*, F Lapenta*, H Gradišar, I Drobnak, J Aupič, Ž Strmšek, D Lainšček, I Hafner-Bratkovič, A Majerle, N Krivec, M Benčina, T Pisanski, TĆ Veličković, A Round, JM Carazo, R Melero, R Jerala
Nature biotechnology, October 2017 (Read more)

Advances in designed bionanomolecular assemblies for biotechnological and biomedical applications
J Snoj*, W Zhou*, A Ljubetič✉, R Jerala✉
Current Opinion in Biotechnology, April 2025 (Read more)

Designed allosteric protein logic
T Plaper, E Merljak, T Fink, T Satler, A Ljubetič, D Lainšček, V Jazbec, M Benčina, S Stevanoska, S Džeroski, R Jerala
Cell Discovery, January 2024 (Read more)

Interpreting neural networks for biological sequences by learning stochastic masks
J Linder, A La Fleur, Z Chen, A Ljubetič, D Baker, S Kannan, G Seelig
Nature machine intelligence, January 2022 (Read more)

Advances in design of protein folds and assemblies.
A Ljubetič, H Gradišar, R Jerala
Current opinion in chemical biology, October 2017

Pre-print articles

2025

De‑novo design of a random protein walker
Liza Ulčakar, Hao Shen, Eva Rajh, Tadej Satler, Federico Alberto Olivieri, Joseph Watson, Yang Hsia, Justin Decarreau, Eric Michael Lynch, Justin Kollman, David Baker, Ajasja Ljubetič✉
BioArxiv, October 2025 (Read more)

All publications

2025

Beyond Dimerization: Harnessing Tetrameric Coiled‑Coils for Nanostructure Assembly
S Vidmar, T Šmidlehner, J Aupič, Ž Strmšek, A Ljubetič, F Xiao, G Hu, C Liu, F Beck, PS Erdmann, R Jerala
Angewandte Chemie International Edition, March 2025 (Read more)

2024

Coupling of Spectrin Repeat Modules for the Assembly of Nanorods and Presentation of Protein Domains
K Mezgec, J Snoj, L Ulčakar, A Ljubetič, M Tušek Žnidarič, M Škarabot, R Jerala
ACS Nano, October 2024 (Read more)

Comparative Simulative Analysis and Design of Single‑Chain Self‑Assembled Protein Cages
F Xiao, L Luo, X Liu, A Ljubetič, N Jin, R Jerala, G Hu
J. Phys. Chem. B, July 2024

2023

2022

Multivalent designed proteins neutralize SARS‑CoV‑2 variants of concern and confer protection against infection in mice
AC Hunt, JB Case, Y-J Park, L Cao, K Wu, AC Walls, Z Liu, JE Bowen, H-W Yeh, S Saini, L Helms, YT Zhao, T-Y Hsiang, TN Starr, I Goreshnik, L Kozodoy, L Carter, R Ravichandran, LB Green, WL Matochko, CA Thomson, B Vögeli, A Krüger, LA VanBlargan, RE Chen, B Ying, AL Bailey, NM Kafai, SE Boyken, A Ljubetič, N Edman, G Ueda, CM Chow, M Johnson, A Addetia, M-J Navarro, N Panpradist, M Gale, BS Freedman, JD Bloom, H Ruohola-Baker, SPJ Whelan, L Stewart, MS Diamond, D Veesler, MC Jewett, D Baker
Science Translational Medicine, April 2022 (Read more)

EMBO Beyond Biology: Connecting peptide, protein, and DNA design with systems chemistry
Dhwanit Dave, Tlalit Massarano, Itai Katzir, Žiga Strmšek, Ajasja Ljubetič, Deborah Sementa
Chem, February 2022 (Read more)

2021

Ensuring Scientific Reproducibility in Bio‑Macromolecular Modeling via Extensive, Automated Benchmarks
J Koehler Leman, S Lyskov, SM Lewis, J Adolf-Bryfogle, RF Alford, K Barlow, Z Ben-Aharon, D Farrell, J Fell, WA Hansen, A Harmalkar, J Jeliazkov, G Kuenze, JD Krys, A Ljubetič, AL Loshbaugh, J Maguire, R Moretti, VK Mulligan, ML Nance, PT Nguyen, S Ó Conchúir, SS Roy Burman, R Samanta, ST Smith, F Teets, JKS Tiemann, A Watkins, H Woods, BJ Yachnin, CD Bahl, C Bailey-Kellogg, D Baker, R Das, F DiMaio, SD Khare, T Kortemme, JW Labonte, K Lindorff-Larsen, J Meiler, W Schief, O Schueler-Furman, JB Siegel, A Stein, V Yarov-Yarovoy, B Kuhlman, A Leaver-Fay, D Gront, JJ Gray, R Bonneau
Nat Commun, November 2021

Designed Folding Pathway of Modular Coiled‑Coil‑Based Proteins
J Aupič, Ž Strmšek, F Lapenta, D Pahovnik, T Pisanski, I Drobnak, A Ljubetič, R Jerala
Nat Commun, February 2021

2019

Functional Self‑Assembled Nanovesicles Based on β‑Cyclodextrin, Liposomes and Adamantyl Guanidines as Potential Nonviral Gene Delivery Vectors
A Štimac, M Tokić, A Ljubetič, T Vuletić, M Šekutor, J Požar, K Leko, M Hanževački, L Frkanec, R Frkanec
Org. Biomol. Chem., May 2019

2018

Polarized Displacement by Transcription Activator‑like Effectors for Regulatory Circuits
T Lebar, A Verbič, A Ljubetič, R Jerala
Nat Chem Biol, November 2018 (Read more)

2017

Advances in design of protein folds and assemblies.
A Ljubetič, H Gradišar, R Jerala
Current opinion in chemical biology, October 2017

Modulation of Coiled‑Coil Dimer Stability through Surface Residues while Preserving Pairing Specificity
I Drobnak, H Gradišar, A Ljubetič, E Merljak, R Jerala
J. Am. Chem. Soc., May 2017 (Read more)