Małgorzata Kotulska

Non-standard proteins in the lens of AlphaFold3 - a case study of amyloids

This paper evaluates AlphaFold3's ability to predict amyloid structures using three datasets, finding it performs better on known fibrillar structures but struggles with non-fibrillar and short fragments.

Aggregating gut: on the link between neurodegeneration and bacterial functional amyloids

The paper identifies gut microbiome functional amyloids and links their abundance to neurodegenerative diseases like Parkinson's and Alzheimer's.

PACT - Prediction of Amyloid Cross-interaction by Threading

PACT predicts amyloid cross-interactions by modeling fibril stability, achieving high AUC and F1 scores on AmyloGraph data and validating interactions between CsgA and Alpha-synuclein.

A Spatiotemporal Reconstruction of the C. elegans Pharyngeal Cuticle Reveals a Structure Rich in Phase-Separating Proteins

The paper reconstructs the spatiotemporal gene expression blueprint for C. elegans pharyngeal cuticle construction and identifies phase-separating proteins involved in cuticle remodeling.