MoiRNAiFold

MoiRNAiFold designs synthetic RNA sequences, particularly riboregulators, using Constraint Programming to satisfy structural and functional constraints for diagnostic and therapeutic applications.

Key Features:

• Constraint Programming Framework: Employs Constraint Programming (CP) with novel variable types, heuristics, and restart strategies for Large Neighborhood Search (LNS).
• Multiple Constraint Handling: Manages multiple design constraints and quality measures simultaneously to tailor RNA designs to specific functional requirements.
• RNA Regulation Control: Includes calculation of Translation Efficiency and other features relevant to RNA regulation control.
• Benchmarking and Performance: Demonstrates superior performance on structural RNA puzzles from EteRNA in benchmark tests compared to previous software.
• Biological Relevance: Produces RNA sequences that have been shown to function in vitro and in vivo as riboregulators controlling gene expression.

Scientific Applications:

• RNA therapeutics and diagnostics: Enables design of synthetic RNA constructs for use in diagnostic and therapeutic applications.
• Riboregulator development: Supports creation of riboregulators to regulate gene expression with specified efficiency and specificity.

Methodology:

Leverages Constraint Programming to systematically explore RNA sequence space and optimize sequences against predefined constraints and quality metrics using novel heuristics and restart strategies for Large Neighborhood Search (LNS).