CyloFold

CyloFold predicts RNA secondary structures with support for arbitrary pseudoknot complexity by simulating coarse-grained folding to identify energetically favorable and sterically feasible helices.

Key Features:

• Unrestricted Pseudoknot Complexity: Handles any level of pseudoknot complexity without imposing algorithmic restrictions on pseudoknot types.
• Coarse-Grained Folding Simulation: Simulates the RNA folding process in a coarse-grained manner and selects helices according to established energy rules.
• Steric Feasibility Testing: Assesses steric feasibility of selected helices using a highly coarse-grained 3D model.
• Competitive Performance: Demonstrated competitive performance against pknotsRG, HotKnots, and UnaFold on datasets of 26 and 241 RNA sequences.

Scientific Applications:

• Analysis of complex pseudoknotted RNAs: Predicts structures for RNA molecules containing intricate pseudoknot interactions that are challenging for traditional methods.
• Study of viral replication and ribosomal function: Facilitates structural analysis relevant to viral RNA elements and ribosomal RNA components.
• Support for RNA-targeted therapeutic research: Provides structural models that can inform development of therapeutics targeting RNA-based mechanisms.

Methodology:

Simulates RNA folding in a coarse-grained manner, selects helices based on energy rules, and verifies steric feasibility using a highly coarse-grained 3D model.