RNAscape

RNAscape visualizes and analyzes RNA tertiary and quaternary structures using topological correspondence to represent three-dimensional organization.

Key Features:

• Topological Mapping Algorithm: Applies a mathematical structural mapping algorithm prioritizing helical segments to preserve tertiary organization and spatial relationships within and between RNA molecules.
• Support for Diverse Structures: Processes 3D structures from Protein Data Bank (PDB) entries or user uploads, supports varied nucleotide types and base-pair annotations, and analyzes RNA/DNA hybrids and DNA topologies including G-quadruplexes.

Scientific Applications:

• RNA Structural Interaction Analysis: Facilitates investigation of tertiary and quaternary RNA interactions to study molecular mechanisms in structural biology, genomics, and transcriptomics.

Methodology:

RNAscape maps three-dimensional RNA coordinates onto topology-preserving representations by emphasizing helical regions and strategically arranging non-helical segments to reduce structural overlap while maintaining correspondence to original spatial organization.