RNApathfinder

RNApathfinder computes near-optimal folding pathways between two specified RNA secondary structures to analyze conformational transitions and their energetics.

Key Features:

• Algorithmic Approach: RNAtabupath employs a tabu semi-greedy heuristic to explore folding-pathway space while avoiding revisiting previously explored suboptimal solutions.
• Performance and Efficiency: Computes folding pathways more rapidly than the barriers program from the Vienna RNA Package, enabling efficient generation of near-optimal pathways.
• Benchmarking and Validation: Demonstrated capability to compute low-energy folding pathways between experimentally known structures of several RNA conformational switches through comparative benchmarking.

Scientific Applications:

• RNA conformational switches: Elucidates folding pathways to study conformational switches involved in gene regulation, viral replication, and cellular signaling.

Methodology:

RNAtabupath applies a tabu semi-greedy heuristic to compute near-optimal folding pathways between two specified RNA secondary structures and has been benchmarked against the barriers program from the Vienna RNA Package; the underlying folding-pathway determination problem is NP-complete.