Aleksandra Elzbieta Badaczewska-Dawid

The paper identifies recurrent duplication of the REST-NOA1 locus in ungulates and shows how structural divergence and regulatory changes contribute to immune system evolution.

The paper presents an enhanced CABS-dock protocol for flexible docking of cyclic peptides to proteins, showing it can sample near-native solutions on benchmark complexes.

The paper presents a database of structure-based protein aggregation predictions for the human proteome using AlphaFold structures and the A3D tool.

The paper introduces Aggrescan3D, a tool for designing protein variants with improved solubility and reduced aggregation using 3D structures, and demonstrates its application on therapeutic proteins.

BIAPSS provides a web platform for analyzing sequence-dependent properties of proteins involved in liquid-liquid phase separation, offering tools for both individual and global sequence analysis.

The paper describes a three-stage protocol for docking peptides to GPCRs using CABS-dock, PD2, and Rosetta FlexPepDock, showing improved accuracy in modeling peptide-GPCR complexes.

The paper describes a workflow to refine protein-peptide complex structures from C-alpha models to high-resolution all-atom models using MODELLER and RosettaFlexPepDock.

The paper presents protocols for simulating protein structure flexibility using CABS-flex and SURPASS, showing CABS-flex's high accuracy compared to experimental and MD data.