Julia K. Varga

The paper maps over 20,000 human protein-protein interactions mediated by short linear motifs using a peptide library screening approach.

PatchMAN2 improves peptide-protein docking efficiency by filtering fragments and focusing sampling on relevant regions, reducing computational cost while maintaining accuracy.

The paper systematically identifies SLiM-binding interactions of USP family auxiliary domains using proteomic and biochemical methods, revealing functional redundancy and motif specificity.

The paper investigates how the SCFDas1 ubiquitin ligase recognizes C-terminal degrons, identifying a conserved binding site and key residues involved in substrate recognition.

This study identifies Gid11 as a substrate receptor for the GID ubiquitin ligase in budding yeast, revealing its role in regulating metabolic transitions by targeting glycolytic factors during ethanol metabolism.

This study shows that SARS-CoV-2 nucleocapsid protein binds to uninfected cells, triggering antibody-mediated complement activation in COVID-19 patients.

The paper identifies conserved mechanisms by which PP2A-B55 substrates bind B55 through α-helices and develops a competitive inhibitor to study its function.

The paper evaluates AlphaFold-Multimer for predicting protein interaction interfaces using short linear motifs and validates some predictions experimentally.

PatchMAN models peptide-protein interactions by aligning structural motifs on the receptor surface, achieving high accuracy in docking without using sequence information.

The paper predicts HDAC6 substrates using a structure-based method calibrated by enzymatic assays, identifies new substrates, and highlights structural determinants of HDAC6 promiscuity.

The paper applies AlphaFold2 to model peptide-protein interactions using a poly glycine linker, showing accurate predictions without sequence alignment.

The paper introduces a web server for predicting crystallization success of transmembrane proteins using a method tailored for membrane proteins.