Kinefold

Kinefold simulates stochastic RNA folding kinetics, including pseudoknots and knots, to model renaturation and co-transcriptional folding of nucleic acids on molecular timescales (seconds to minutes).

Key Features:

• Stochastic folding simulations: Simulates renaturation and co-transcriptional folding paths by modeling helix formation and dissociation events for RNA sequences.
• Pseudoknot and knot prediction: Predicts pseudoknots and topologically entangled helices (knots) using simple geometrical and topological constraints.
• Time-resolved kinetics: Operates on molecular timescales ranging from seconds to minutes to capture dynamic folding processes.
• Comprehensive output: Produces series of low free energy structures, an online animated folding path, and programmable trajectory plots that focus on specific helices.

Scientific Applications:

• RNA folding kinetics: Analysis of folding pathways and kinetic intermediates for RNA sequences at relevant molecular timescales.
• Pseudoknot and knot structural analysis: Investigation of the formation, stability, and topological properties of pseudoknots and knots in RNA.
• Co-transcriptional and renaturation dynamics: Modeling of folding during transcription and renaturation processes to study pathway dependence and structural outcomes.

Methodology:

Uses stochastic modeling of helix formation and dissociation events and incorporates geometrical and topological constraints to predict pseudoknots and knots.