Francesco Costa

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.

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.

NERVE 2.0: boosting the New Enhanced Reverse Vaccinology Environment via artificial intelligence and a user-friendly web interface

NERVE 2.0 improves vaccine candidate identification through AI models and a user-friendly web interface, outperforming previous versions and other RV tools.

Temporal GWAS identifies a widely distributed novel protein Stv contributing to pathogen success in Shigella spp.

The paper identifies a novel protein Stv associated with Shigella's success through temporal GWAS, showing its presence in expanding lineages and other bacterial species.