RNAxplorer

RNAxplorer: Adaptive Sampling of RNA Energy Landscapes

RNAxplorer performs adaptive sampling of RNA secondary structures to approximate RNA folding kinetics by exploring the conformational energy landscape and generating representative structure ensembles.

Key Features:

• Adaptive Sampling: Implements dynamic programming–based Boltzmann sampling with guiding potentials incorporated as pseudo-energy terms to bias sampling away from previously explored structures.
• Guiding Potentials: Accumulates structure similarity–based pseudo-energy terms to steer exploration toward underrepresented regions of RNA structure space.
• Diverse Structure Generation: Identifies rare conformations and key kinetic traps, enabling representative coarse graining of RNA folding landscapes.
• Benchmarked Performance: Demonstrates improved structural diversity and enhanced approximation of RNA folding kinetics relative to alternative sampling methods.

Scientific Applications:

• RNA Folding Dynamics: Supports analysis of RNA conformational landscapes, kinetic traps, and mechanisms underlying RNA function and stability.

Methodology:

RNAxplorer applies dynamic programming to perform Boltzmann sampling of RNA secondary structures under adaptive guiding potentials encoded as pseudo-energy terms. These potentials iteratively penalize similarity to previously sampled structures, promoting exploration of distinct conformations and enabling kinetic landscape approximation.