Ligand-binding pockets in RNA, and where to find them.

ABSTRACT: RNAs are critical regulators of gene expression, and their functions are often mediated by complex secondary and tertiary structures. Structured regions in RNA can selectively interact with small molecules - via well-defined ligand binding pockets - to modulate the regulatory repertoire of an RNA. The broad potential to modulate biological function intentionally via RNA-ligand interactions remains unrealized, however, due to challenges in identifying compact RNA motifs with the ability to bind ligands with good physicochemical properties (often termed drug-like). Here, we devise fpocketR, a computational strategy that accurately detects pockets capable of binding drug-like ligands in RNA structures. Remarkably few, roughly 50, of such pockets have ever been visualized. We experiment

SUBMITTER: Veenbaas SD 

PROVIDER: S-EPMC11952572 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature