78 citations · 161 across the 10 of their papers we have counts for
10 papers
Zero-shot protein stability prediction by inverse folding models: a free energy interpretation
Jes Frellsen, Maher M. Kassem, Tone Bengtsen +4
Inverse folding models have proven to be highly effective zero-shot predictors of protein stability. Despite this success, the link between the amino acid preferences of an inverse…
Probabilistic thermal stability prediction through sparsity promoting transformer representation
Yevgen Zainchkovskyy, Jesper Ferkinghoff-Borg, Anja Bennett +5
Pre-trained protein language models have demonstrated significant applicability in different protein engineering task. A general usage of these pre-trained transformer models laten…
Potentials of Mean Force for Protein Structure Prediction Vindicated, Formalized and Generalized
Thomas Hamelryck, Mikael Borg, Martin Paluszewski +6
Understanding protein structure is of crucial importance in science, medicine and biotechnology. For about two decades, knowledge based potentials based on pairwise distances -- so…
Stop-and-go kinetics in amyloid fibrillation
Jesper Fonslet, Christian Beyschau Andersen, Sandeep Krishna +6
Many human diseases are associated with protein aggregation and fibrillation. We present experiments on in vitro glucagon fibrillation using total internal reflection fluorescence…
What thermodynamic features characterize good and bad folders? Results from a simplified off-lattice protein model
A. Amatori, J. Ferkinghoff-Borg, G. Tiana +1
The thermodynamics of the small SH3 protein domain is studied by means of a simplified model where each bead-like amino acid interacts with the others through a contact potential c…
Scale Free Cluster Distributions from Conserving Merging-Fragmentation Processes
Jesper Ferkinghoff-Borg, Mogens H. Jensen, Joachim Mathiesen +1
We propose a dynamical scheme for the combined processes of fragmentation and merging as a model system for cluster dynamics in nature and society displaying scale invariant proper…