Nucleases-enzymes that catalyze the cleavage of RNA or DNA phosphodiester bondsplay essential roles in a large number of key biological processes, e.g. DNA replication, recombination and repair, DNA topoisomerization and RNA processing, maturation and splicing. While they all cleave phosphodiester bonds, they present a broad diversity of structures and of mechanisms, that can either be ion-independent or rely on 1 or 2 ionstypically Mg 2+ -for catalysis. Given the importance of these processes, there is a pronounced interest in better understanding them at a molecular level, which is where molecular simulations can bring valuable additional insights.