Inversion of the Balance between Hydrophobic and Hydrogen Bonding Interactions in Protein Folding and Aggregation. - Anthony W. Fitzpatrick; Tuomas P. J. Knowles; Christopher A. Waudby; Michele Vendruscolo; Christopher M. Dobson (PLoS Comput. Biol., 2011)

Connecting Macroscopic Observables and Microscopic Assembly Events in Amyloid Formation Using Coarse Grained Simulations. - Noah S. Bieler; Tuomas P. J. Knowles; Daan Frenkel; Robert Vácha (PLoS Comput. Biol., 2012)

Easyworm: an open-source software tool to determine the mechanical properties of worm-like chains. - Guillaume Lamour; Julius B. Kirkegaard; Hongbin Li; Tuomas P. J. Knowles; Jörg Gsponer (Source Code Biol. Medicine, 2014)

Oligomers of Heat-Shock Proteins: Structures That Don't Imply Function. - William M. Jacobs; Tuomas P. J. Knowles; Daan Frenkel (PLoS Comput. Biol., 2016)

Learning the rules of peptide self-assembly through data mining with large language models. - Zhenze Yang; Sarah K. Yorke; Tuomas P. J. Knowles; Markus J. Buehler (CoRR, 2024)

Multi-state Protein Design with DynamicMPNN. - Alex Abrudan; Sebastian Pujalte Ojeda; Chaitanya K. Joshi; Matthew Greenig; Felipe Engelberger; Alena Khmelinskaia; Jens Meiler; Michele Vendruscolo; Tuomas P. J. Knowles (CoRR, 2025)