Joanna Ida Sulkowska

Multi-barrier unfolding of the double-knotted protein, TrmD-Tm1570, revealed by single-molecule force spectroscopy and molecular dynamics

This study uses single-molecule force spectroscopy and molecular dynamics to analyze the unfolding and folding of double-knotted and single-knotted proteins, revealing that double-knotted proteins require chaperone assistance for full knotting.

Universe of Lasso Proteins: Exploring the limit of entanglement and folding landscape of proteins predicted by AlphaFold

The paper uses AlphaFold to analyze protein structures and identifies new lasso motifs, including knotted lasso proteins, and explores their topological complexity and conservation.

Knotted artifacts in predicted 3D RNA structures

The paper analyzes 3D RNA structure prediction models from CASP15 and finds that all entanglements are artifacts, with ML methods more prone to generating them than traditional methods.

Knot or Not? Sequence-Based Identification of Knotted Proteins With Machine Learning

This study uses machine learning to predict protein knotting from amino acid sequences, achieving 98.5% accuracy using AlphaFold predictions and UniProt data.

New 63 knot and other knots in human proteome from AlphaFold predictions

The paper analyzes AlphaFold-predicted human protein structures to identify knots, finding 65 robustly knotted proteins, including a new complex knot type.