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33. Single-molecule imaging and molecular dynamics simulations reveal early activation of the MET receptor in cells.
Yunqing Li‡, Serena M. Arghittu‡, Marina S. Dietz, Gabriel J. Hella, Daniel Haße, Davide M. Ferraris, Petra Freund, Hans-Dieter Barth, Luisa Iamele, Hugo de Jonge, Hartmut H. Niemann, Roberto Covino, Mike Heilemann (‡shared first authors)
Nature Communications 15 9486 (2024)
32. Amortized template-matching of molecular conformations from cryo-electron microscopy images using simulation-based inference.
Lars Dingeldein, David Silva-Sánchez, Luke Evans, Edoardo D’Imprima, Nikolaus Grigorieff, Roberto Covino‡, Pilar Cossio‡ (‡shared corresponding authors).
bioRxiv preprint (2024)
31. Free energy, rates, and mechanism of transmembrane dimerization in lipid bilayers from dynamically unbiased molecular dynamics simulations.
Emil Jackel, Gianmarco Lazzeri, Roberto Covino.
arXiv preprint (2024)
30. Making lipids very unhappy to discover how they bind to proteins.
Chris Stefan and Roberto Covino.
Journal of Cell Biology 223 (11): e202410022 (2024)
29. Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering
Paulina Kettel, Laura Marosits, Elena Spinetti, Michael Rechberger, Caterina Giannini, Philipp Radler, Isabell Niedermoser, Irmgard Fischer, Gijs A Versteeg, Martin Loose, Roberto Covino, Gulsun Elif Karagoz.
The EMBO Journal 43: 4668 – 4698 (2024)
28. Sampling a Rare Protein Transition Using Quantum Annealing
Danial Ghamari, Roberto Covino, Pietro Faccioli.
J. Chem. Theory Comput. 20, 8, 3322-3334 (2024)
27. Understanding the cell: future views of structural biology
Marin Beck‡, Roberto Covino‡, Inga Hänelt‡, Michaela Müller-McNicoll‡ (‡shared corresponding authors, names in alphabetical order).
Cell 187 3 545-562 (2024)
26. Membrane association of the ATG8 conjugation machinery emerges as a key regulatory feature for autophagosome biogenesis
Sharon A. Tooze, Wenxin Zhang, Gianmarco Lazzeri, Deepanshi Gahlot, Lipi Thukral, Roberto Covino, Taki Nishimura.
FEBS Lett, 598: 107-113 (2024)
25. ATG3 proteins possess a unique amphipathic α-helix essential for the Atg8/LC3 lipidation reaction
Taki Nishimura, Gianmarco Lazzeri, Sharon A. Tooze, Roberto Covino.
Autophagy 20(1), 212–213 (2023)
24. Molecular free energies, rates, and mechanisms from data-efficient path sampling simulations
Gianmarco Lazzeri, Hendrik Jung, Peter G. Bolhuis, Roberto Covino.
J. Chem. Theory Comput., 19, 24, 9060–9076 (2023) – arXiv preprint
23. Machine-guided path sampling to discover mechanisms of molecular self-organization
Hendrik Jung*, Roberto Covino*, A. Arjun, Christian Leitold, Christoph Dellago, Peter G. Bolhuis & Gerhard Hummer (*shared first authors).
Nature Computational Science 3, 334–345 (2023)
22. Unique Amphipathic α-helix Drives Membrane Insertion and Enzymatic Activity of ATG3
Taki Nishimura†, Gianmarco Lazzeri, Noboru Mizushima, Roberto Covino†, Sharon Tooze. (†shared corresponding authors)
Science Advances 9,eadh1281 (2023) — bioRxiv preprint
21. Antibody accessibility
determines location of spike surface mutations in
SARS-CoV-2 variants
Sören von Bülow, Mateusz Sikora, Florian E. C. Blanc, Roberto Covino, Gerhard Hummer.
PLoS Comput Biol 19(1): e1010822 (2023)
20. Simulation-based inference of single-molecule force spectroscopy
Lars Dingeldein, Pilar Cossio, Roberto Covino.
Mach. Learn.: Sci. Technol. 4 025009 (2023) — arXiv preprint
19. Sampling Rare Conformational Transitions with a Quantum Computer
Danial Ghamari, Philipp Hauke, Roberto Covino†, Pietro Faccioli† (†shared corresponding authors).
Scientific Reports 12, 16336 (2022) — arXiv preprint
18. Information-theoretical measures identify accurate low-resolution representations of protein configurational space
Margherita Mele, Roberto Covino, Raffaello Potestio.
Soft Matter, 18, 7064-7074 (2022) — arXiv preprint
17. Autonomous artificial intelligence discovers mechanisms of molecular self-organization in virtual experiments
Hendrik Jung*, Roberto Covino*, A Arjun, Peter G. Bolhuis, Gerhard Hummer (*shared first authors).
arXiv preprint
16. The evolutionary making of SARS-CoV-2
Ruben Iruegas, Julian Dosch, Mateusz Sikora, Gerhard Hummer, Roberto Covino, Ingo Ebersberger.
bioRxiv preprint
15. Cysteine crosslinking in native membranes establishes the transmembrane architecture of Ire1
Kristina Väth, Carsten Mattes, John Reinhard, Roberto Covino, Heike Stumpf, Gerhard Hummer, and Robert Ernst.
Journal of Cellular Biology 220 (8): e202011078 (2021)
14. Computational epitope map of SARS-CoV-2 spike protein
Mateusz Sikora*, Florian E. C. Blanc*, Sören von Bülow*, Michael Gecht*, Roberto Covino*, and Gerhard Hummer (*shared first authors).
PLoS Comput Biol 17(4): e1008790 (2021) — bioRxiv preprint
13. In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges
Beata Turoňová, Mateusz Sikora, Christoph Schürmann, Wim J. H. Hagen, Sonja Welsch, Florian E. C. Blanc, Sören von Bülow, Michael Gecht, Katrin Bagola, Cindy Hörner, Ger van Zandbergen, Jonathan Landry, Nayara Trevisan Doimo de Azevedo, Shyamal Mosalaganti, Andre Schwarz, Roberto Covino, Michael D. Mühlebach, Gerhard Hummer, Jacomine Krijnse Locker, and Martin Beck.
Science 370(6513) 203 (2020) — Cover article (issue 08.10.2020)
Long coverage on the Frankfurter Allgemeine Zeitung and the New York Times.
12. Regulation of lipid saturation without sensing membrane fluidity
Stephanie Ballweg, Erdinc Sezgin, Milka Doktorova, Roberto Covino, John Reinhard, Dorith Wunnicke, Inga Hänelt, Ilya Levental, Gerhard Hummer, and Robert Ernst.
Nature Communications 11 756 (2020)
11. Molecular free energy profiles from force spectroscopy experiments by inversion of observed committors
Roberto Covino*, Michael T. Woodside, Gerhard Hummer, Attila Szabo, and Pilar Cossio* (*shared corresponding authors).
Journal of Chemical Physics 151 154115 (2019) – Featured article
10. Osh proteins control nanoscale lipid organization necessary for PI(4,5)P2 synthesis
Taki Nishimura, Michael Gecht, Roberto Covino, Gerhard Hummer, Hiroyuki Arai, Nozomu Kono, and Christopher J. Stefan.
Molecular Cell 75(5) 1043 (2019)
9. The active roles of biological membranes and the hidden side of the unfolded protein response
Roberto Covino, Gerhard Hummer, and Robert Ernst.
Molecular Cell 71(3) 458 (2018)
8. The molecular recognition of phosphatidic acid by an amphipathic helix in Opi1
Harald F. Hofbauer, Michael Gecht, Sabine C. Fischer, Anja Seybert, Achilleas S. Frangakis, Ernst H.K. Stelzer, Roberto Covino, Gerhard Hummer, and Robert Ernst.
Journal of Cell Biology 217(9) 3109-3126 (2018)
7. Variational identification of markovian transition states
Linda Martini, Adam Kells, Roberto Covino, Gerhard Hummer, Nicolae-Viorel Buchete, and Edina Rosta.
Physical Review X 7(3) 031060 (2017)
6. Activation of the unfolded protein response by lipid bilayer stress
Kristina Halbleib, Kristina Pesek, Roberto Covino, Harald F. Hofbauer, Dorith Wunnicke, Inga Hanelt, Gerhard Hummer, and Robert Ernst.
Molecular Cell 67(4) 673 (2017)
Featured in Nature Reviews Molecular Cell Biology 18 471 (2017)
5. Intrinsic map dynamics exploration for uncharted effective free-energy landscapes
Eliodoro Chiavazzo, Roberto Covino, Ronald R. Coifman, C. William Gear, Anastasia S. Georgiou, Gerhard Hummer, and Ioannis G. Kevrekidis.
PNAS 114(28) E5494 (2017)
4. A eukaryotic sensor for membrane lipid saturation
Roberto Covino*, Stephanie Ballweg*, Claudius Stordeur*, Jonas B. Michaelis, Kristina Puth, Florian Wernig, Amir Bahrami, Andreas M. Ernst, Gerhard Hummer, and Robert Ernst (*shared first authors).
Molecular Cell 63(1) 49 (2016)
3. The role of non-native interactions in the folding of knotted proteins: insights from molecular dynamics simulations
Roberto Covino*, Tatjana Škrbić, Silvio a Beccara, Pietro Faccioli, and Cristian Micheletti (*corresponding author).
Biomolecules 4(1) 1 (2013)
2. Folding pathways of a knotted protein with a realistic atomistic force field
Silvio a Beccara, Tatjana Škrbić, Roberto Covino, Cristian Micheletti, and Pietro Faccioli.
PLoS Comput Biol 9(3) e1003002 (2013)
1. Dominant folding pathways of a WW domain
Silvio a Beccara, Tatjana Škrbić, Roberto Covino, and Pietro Faccioli.
PNAS 109(7) 2330 (2012)