RNANR

RNANR generates locally optimal RNA secondary structures under the Nussinov energy model to explore kinetic landscapes using exhaustive enumeration and non-redundant stochastic sampling.

Key Features:

• Locally Optimal Structure Enumeration: Exhaustively enumerates locally optimal secondary structures to characterize significant kinetic basins in RNA folding landscapes.
• Non-Redundant Stochastic Sampling: Implements stochastic sampling that minimizes redundant structures, enhancing coverage of unique intermediate conformations and providing structural parameters for comparative analysis.

Scientific Applications:

• RNA Folding Kinetics Analysis: Supports out-of-equilibrium studies and investigation of riboswitch dynamics through detailed exploration of RNA kinetic landscapes.

Methodology:

RNANR applies the Nussinov energy model to enumerate locally optimal secondary structures and combines exhaustive enumeration with non-redundant stochastic sampling to efficiently characterize unique conformations within RNA kinetic landscapes.