RAG

RNA-As-Graphs (RAG): RNA secondary structure analysis and design using tree graph representations

RNA-As-Graphs (RAG) applies graph theory to represent RNA secondary structures as coarse-grained tree graphs, enabling prediction of tertiary topologies and design of RNA sequences based on structural topology.

Key Features:

• RAG Sampler: Samples tree graph topologies from RNA secondary structures to predict corresponding tertiary topologies through graph-based representations.
• RAG Builder: Constructs three-dimensional atomic models from candidate tree graphs to generate spatial RNA structural models.
• RAG Designer: Designs RNA sequences predicted to fold into specified tree graph topologies, enabling generation of novel RNA motifs.

Scientific Applications:

• Tertiary Structure Prediction: Predicts RNA tertiary structures from known secondary structures to analyze RNA folding mechanisms.
• RNA Motif Engineering: Designs novel RNA sequences with defined structural motifs for applications in synthetic biology and therapeutic development.

Methodology:

Represents RNA secondary structures as coarse-grained tree graphs and applies graph theory to analyze topological features, enabling computational sampling, topology-based tertiary prediction, and sequence design through systematic manipulation of graph representations.