Publications

Bauer, M. S.; Gruber, S.; Hausch, A.; Melo, M. C. R.; Gomes, P. S. F. C.; Nicolaus, T.; Milles, L. F.; Gaub, H. E.; Bernardi, R. C.; Lipfert, J.: Single-molecule force stability of the SARS-CoV-2–ACE2 interface in variants-of-concern. Nature Nanotechnology (3), pp. 399 - 405 (2024)

Sumida, K. H.; Núñez-Franco, R.; Kalvet, I.; Pellock, S. J.; Wicky, B. I. M.; Milles, L. F.; Dauparas, J.; Wang, J.; Kipnis, Y.; Jameson, N. et al.; Kang, A.; De La Cruz, J.; Sankaran, B.; Bera, A. K.; Jiménez-Osés, G.; Baker, D.: Improving Protein Expression, Stability, and Function with ProteinMPNN. Journal of the American Chemical Society (3), pp. 2054 - 2061 (2024)

An, L.; Hicks, D. R.; Zorine, D.; Dauparas, J.; Wicky, B. I. M.; Milles, L. F.; Courbet, A.; Bera, A. K.; Nguyen, H.; Kang, A. et al.; Carter, L.; Baker, D.: Hallucination of closed repeat proteins containing central pockets. Nature Structural & Molecular Biology (11), pp. 1755 - 1760 (2023)

Doyle, L. A.; Takushi, B.; Kibler, R. D.; Milles, L. F.; Orozco, C. T.; Jones, J. D.; Jackson, S. E.; Stoddard, B. L.; Bradley, P.: De novo design of knotted tandem repeat proteins. Nature Communications 14, 6746 (2023)

Kim, D. E.; Jensen, D. R.; Feldman, D.; Tischer, D.; Saleem, A.; Chow, C. M.; Li, X.; Carter, L.; Milles, L.; Nguyen, H. et al.; Kang, A.; Bera, A. K.; Peterson, F. C.; Volkman, B. F.; Ovchinnikov, S.; Baker, D.: De novo design of small beta barrel proteins. Proceedings of the National Academy of Sciences (11), e2207974120 (2023)

Watson, J. L.; Juergens, D.; Bennett, N. R.; Trippe, B. L.; Yim, J.; Eisenach, H. E.; Ahern, W.; Borst, A. J.; Ragotte, R. J.; Milles, L. F. et al.; Wicky, B. I. M.; Hanikel, N.; Pellock, S. J.; Courbet, A.; Sheffler, W.; Wang, J.; Venkatesh, P.; Sappington, I.; Torres, S. V.; Lauko, A.; De Bortoli, V.; Mathieu, E.; Ovchinnikov, S.; Barzilay, R.; Jaakkola, T. S.; DiMaio, F.; Baek, M.; Baker, D.: De novo design of protein structure and function with RFdiffusion. Nature (7976), pp. 1089 - 1100 (2023)

Bauer, M. S.; Gruber, S.; Hausch, A.; Gomes, P. S. F. C.; Milles, L. F.; Nicolaus, T.; Schendel, L. C.; Navajas, P. L.; Procko, E.; Lietha, D. et al.; Melo, M. C. R.; Bernardi, R. C.; Gaub, H. E.; Lipfert, J.: A tethered ligand assay to probe SARS-CoV-2:ACE2 interactions. Proceedings of the National Academy of Sciences 119 (14), e2114397119 (2022)

Dauparas, J.; Anishchenko, I.; Bennett, N.; Bai, H.; Ragotte, R. J.; Milles, L. F.; Wicky, B. I. M.; Courbet, A.; de Haas; J., R. et al.; Bethel, N.; Leung, P. J. Y.; Huddy, T. F.; Pellock, S.; Tischer, D.; Chan, F.; Koepnick, B.; Nguyen, H.; Kang, A.; Sankaran, B.; Bera, A. K.; King, N. P.; Baker, D.: Robust deep learning–based protein sequence design using ProteinMPNN. Science 378 (6615), pp. 49 - 56 (2022)

Wang, J.; Lisanza, S.; Juergens, D.; Tischer, D.; Watson, J. L.; Castro, K. M.; Ragotte, R.; Saragovi, A.; Milles, L. F.; Baek, M. et al.; Anishchenko, I.; Yang, W.; Hicks, D. R.; Expòsit, M.; Schlichthaerle, T.; Chun, J.-H.; Dauparas, J.; Bennett, N.; Wicky, B. I. M.; Muenks, A.; DiMaio, F.; Correia, B.; Ovchinnikov, S.; Baker, D.: Scaffolding protein functional sites using deep learning. Science 377 (6604), pp. 387 - 394 (2022)

Wicky, B. I. M.; Milles, L. F.; Courbet, A.; Ragotte, R. J.; Dauparas, J.; Kinfu, E.; Tipps, S.; Kibler, R. D.; Baek, M.; DiMaio, F. et al.; Li, X.; Carter, L.; Kang, A.; Nguyen, H.; Bera, A. K.; Baker, D.: Hallucinating symmetric protein assemblies. Science 378 (6615), pp. 56 - 61 (2022)

Kluger, C.; Braun, L.; Sedlak, S. M.; Pippig, D. A.; Bauer, M. S.; Miller, K.; Milles, L. F.; Gaub, H. E.; Vogel, V.: Different Vinculin binding sites use the same mechanism to regulate directional force transduction. Biophysical Journal 118 (6), pp. 1344 - 1356 (2020)

Milles, L. F.; Gaub, H. E.: Extreme mechanical stability in protein complexes. Current Opinion in Structural Biology 60, pp. 124 - 130 (2020)

Bauer, M. S.; Baumann, F.; Daday, C.; Redondo, P.; Durner, E.; Jobst, M. A.; Milles, L. F.; Mercadante, D.; Pippig, D. A.; Gaub, H. E. et al.; Gräter, F.; Lietha, D.: Structural and mechanistic insights into mechanoactivation of focal adhesion kinase. Proceedings of the National Academy of Sciences 116 (14), pp. 6766 - 6774 (2019)

Erlich, K. R.; Sedlak, S. M.; Jobst, M. A.; Milles, L. F.; Gaub, H. E.: DNA-free directed assembly in single-molecule cut-and-paste. Nanoscale 11, pp. 407 - 411 (2019)

Vanderlinden, W.; Brouns, T.; Walker, P. U.; Kolbeck, P. J.; Milles, L. F.; Ott, W.; Nickels, P. C.; Debyser, Z.; Lipfert, J.: The free energy landscape of retroviral integration. Nature Communications 10, 4738 (2019)

Milles, L. F.; Schulten, K.; Gaub, H. E.; Bernardi, R. C.: Molecular mechanism of extreme mechanostability in a pathogen adhesin. Science 359 (6383), pp. 1527 - 1533 (2018)

Milles, L. F.; Unterauer, E. M.; Nicolaus, T.; Gaub, H. E.: Calcium stabilizes the strongest protein fold. Nature Communications 9, 4764 (2018)

Brand, U.; Gao, S.; Engl, W.; Sulzbach, T.; Stahl, S. W.; Milles, L. F.; Nesterov, V.; Li, Z.: Comparing AFM cantilever stiffness measured using the thermal vibration and the improved thermal vibration methods with that of an SI traceable method based on MEMS. Measurement Science and Technology 28 (3), 034010 (2017)

Ott, W.; Jobst, M. A.; Bauer, M. S.; Durner, E.; Milles, L. F.; Nash, M. A.; Gaub, H. E.: Elastin-like Polypeptide Linkers for Single-Molecule Force Spectroscopy. ACS Nano 11 (6), pp. 6346 - 6354 (2017)

Sedlak, S. M.; Bauer, M. S.; Kluger, C.; Schendel, L. C.; Milles, L. F.; Pippig, D. A.; Gaub, H. E.: Monodisperse measurement of the biotin-streptavidin interaction strength in a well-defined pulling geometry. PLoS ONE 12 (2), e0188722 (2017)

Milles, L. F.; Bayer, E. A.; Nash, M. A.; Gaub, H. E.: Mechanical Stability of a High-Affinity Toxin Anchor from the Pathogen Clostridium perfringens. The Journal of Physical Chemistry B 121 (15), pp. 3620 - 3625 (2016)

Aschenbrenner, D.; Baumann, F.; Milles, L. F.; Pippig, D. A.; Gaub, H. E.: C-5 Propynyl Modifications Enhance the Mechanical Stability of DNA. ChemPhysChem 16 (10), pp. 2085 - 2090 (2015)

Baumann, F.; Bauer, M. S.; Milles, L. F.; Alexandrovich, A.; Gaub, H. E.; Pippig, D. A.: Monovalent Strep-Tactin for strong and site-specific tethering in nanospectroscopy. Nature Nanotechnology 11, pp. 89 - 94 (2015)

Jobst, M. A.; Milles, L. F.; Schoeler, C.; Ott, W.; Fried, D. B.; Bayer, E. A.; Gaub, H. E.; Nash, M. A.: Resolving dual binding conformations of cellulosome cohesin-dockerin complexes using single-molecule force spectroscopy. eLife 4, e10319 (2015)

Klamecka, K.; Severin, P. M.; Milles, L. F.; Gaub, H. E.; Leonhardt, H.: Energy profile of nanobody–GFP complex under force. Physical Biology 12 (5), 056009 (2015)

Malinowska, K. H.; Verdorfer, T.; Meinhold, A.; Milles, L. F.; Funk, V.; Gaub, H. E.; Nash, M. A.: Redox-Initiated Hydrogel System for Detection and Real-Time Imaging of Cellulolytic Enzyme Activity. ChemSusChem (10), pp. 2825 - 2831 (2014)

Otten, M.; Ott, W.; Jobst, M. A.; Milles, L. F.; Verdorfer, T.; Pippig, D. A.; Nash, M. A.; Gaub, H. E.: From genes to protein mechanics on a chip. Nature Methods (11), pp. 1127 - 1130 (2014)

Schoeler, C.; Malinowska, K. H.; Bernardi, R. C.; Milles, L. F.; Jobst, M. A.; Durner, E.; Ott, W.; Fried, D. B.; Bayer, E. A.; Schulten, K. et al.; Gaub, H. E.; Nash, M. A.: Ultrastable cellulosome-adhesion complex tightens under load. Nature Communications 5, 5635 (2014)

Verkuil, R.; Kabeli, O.; Du, Y.; Wicky, B. I. M.; Milles, L. F.; Dauparas, J.; Baker, D.; Ovchinnikov, S.; Sercu, T.; Rives, A.: Language models generalize beyond natural proteins. bioRxiv (2022)

Milles, L. F.; Gaub, H. E.: Is mechanical receptor ligand dissociation driven by unfolding or unbinding? bioRxiv (2019)

Bauer, M. S.; Milles, L. F.; Sedlak, S. M.; Gaub, H. E.: Monomeric streptavidin: a versatile regenerative handle for force spectroscopy. bioRxiv (2018)