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

2026

Prosculpt: Lowering the Barrier to Computational Protein Design
Federico A Olivieri*, Alina Konstantinova*, Neža Ribnikar, Nej Bizjak, Žan Žnidar, Kiyan Abel, Eva Rajh, Ajasja Ljubetič✉
BioArxiv, June 2026 (Read more)

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)