RPocket

RPocket analyzes and catalogs RNA pocket structures and RNA–ligand interactions to support structural and functional characterization of RNA binding sites.

Key Features:

• RNA Pocket Topology and Geometry: Provides geometrical size, centroid, shape, and associated secondary structure elements for 240 RNA pockets derived from 94 non-redundant RNA–ligand complex structures, quantified using the RPDescriptor algorithm.
• RNA–Ligand Interaction Annotation: Integrates atom-level and nucleotide-level interaction data, including electrostatic, van der Waals, and hydrophobic contacts, to characterize functional binding sites and topological patterns.

Scientific Applications:

• RNA Structural Modeling and Ligand Design: Supports RNA tertiary structure prediction and rational design of ligands targeting RNA pockets using geometrical descriptors and interaction constraints.

Methodology:

RPocket extracts RNA pocket data from curated non-redundant RNA–ligand complex structures and computes quantitative geometrical descriptors with RPDescriptor, integrating sequence, secondary structure, and tertiary interaction information to analyze RNA pocket topology and binding mechanisms.