RNAspider

RNAspider identifies and classifies entanglements in RNA three-dimensional (3D) structures to analyze and characterize primary and higher-order topological interactions.

Key Features:

• Automatic Identification and Classification: Automates detection of primary and higher-order entanglements in RNA 3D structures and classifies them using a topology- and structural-element-based scheme.
• Visualization Capabilities: Provides visualization of entanglements and complex topologies, including pseudoknotted configurations.
• Support for Diverse Models: Analyzes both experimentally determined 3D models and computationally predicted RNA 3D structures.

Scientific Applications:

• Analysis of RNA topologies: Enables characterization of primary and higher-order topological interactions and knot-like folds in RNA molecules.
• Study of pseudoknots: Facilitates identification and visualization of pseudoknotted configurations relevant to viral genomes.
• Structural genomics and virology: Supports structural-genomics investigations and analyses of RNA viruses by revealing entanglement-derived motifs.
• Therapeutic development: Informs strategies targeting RNA-based mechanisms by identifying structural motifs and entanglements.

Methodology:

Automated detection and classification of RNA entanglements using a topology- and structural-element-based classification, with visualization of identified entanglements, applied to experimentally obtained and computationally predicted 3D models.