Antonina E. Andreeva

Large-scale structure prediction of DUF-containing protein-protein interactions

A logistic regression on STRING evidence picked DUF (domain of unknown function) protein pairs for AlphaFold 3; of 12,298 modelled pairs, 1,208 met strict and 2,433 liberal confidence.

A global survey of intramolecular isopeptide bonds

The paper identifies and characterizes intramolecular isopeptide bonds in protein domains across organisms, revealing their structural and functional significance.

A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions

The paper presents a global virome atlas, UHGV, and identifies genomic factors influencing phage-host interactions.

A defining member of the new cysteine-cradle family is an aECM protein signalling skin damage in C. elegans

The paper identifies spia-1 as a gene involved in immune activation in C. elegans by sensing cuticle damage through its secreted protein with a novel cysteine-cradle domain.

Isopeptor: a tool for detecting intramolecular isopeptide bonds in protein structures

Isopeptor detects intramolecular isopeptide bonds in protein structures using structure-guided template matching and logistic regression, achieving high recall and precision on a curated PDB subset.

A comparative study of the cryo-EM structures of S. cerevisiae and human anaphase-promoting complex/cyclosome (APC/C)

This study compares cryo-EM structures of S. cerevisiae and human APC/C complexes, revealing conserved architectures and differences in regulatory mechanisms.