Kirill E. Medvedev

Domain classification of archaeal proteomes reveals conserved fold repertoire

The paper classifies archaeal proteomes at the domain level, revealing that structural diversity is conserved across archaea and that unclassified proteins are due to classification limitations, not structural novelty.

Bacterial Schlafens mediate anti-phage defense

This study identifies bacterial Schlafen nucleases as antiviral effectors that target phage infection by cleaving tRNA and inducing abortive infection.

Leveraging AI to Explore Structural Contexts of Post-Translational Modifications in Drug Binding

This paper uses AI to predict how post-translational modifications affect drug binding by modeling PTM-modified protein structures and ligand interactions.

DrugDomain 2.0: comprehensive database of protein domains-ligands/drugs interactions across the whole Protein Data Bank

DrugDomain 2.0 maps protein domain-ligand interactions across the Protein Data Bank, integrating experimental and AI-predicted data for over 37,000 ligands and 7,560 drugs.

DrugDomain: the evolutionary context of drugs and small molecules bound to domains

DrugDomain provides a database of interactions between DrugBank molecules and ECOD domains of human proteins, using experimental structures and AlphaFold models.

Structure classification of the proteins from Salmonella enterica pangenome revealed novel potential pathogenicity islands

The paper classifies proteins from Salmonella enterica pangenome, identifies potentially pathogenic proteins, and reveals their clustering in the genome.

ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM

The paper classifies domains in 48 proteomes from the AlphaFold Database using DPAM, finding differences in domain composition between eukaryotes and bacteria.