# List of RNA structure prediction software ## Links (Wikipedia order) <!-- injected from _registry/childlinks/List_of_RNA_structure_prediction_software.json (2026-07-30T02:09:12Z) --> `Ajax_(programming)` · `Backtracking` · [[Comparison_of_nucleic_acid_simulation_software]] · [[Comparison_of_software_for_molecular_mechanics_modeling]] · `Constraint_programming` · `D3.js` · `DECIPHER_(software)` · [[Dynamic_programming]] · `Emacs` · `Gibbs_free_energy` · `Google_Developers` · `HMMER` · `Java_(programming_language)` · `Markov_chain_Monte_Carlo` · `Metaheuristic` · `MicroRNA` · `Multiple_sequence_alignment` · `NUPACK` · `Newtonian_dynamics` · `Non-coding_RNA` · `Nucleic_acid_structure_prediction` · `Perl` · `Pseudoknot` · `Python_(programming_language)` · `RNA` · `Rfam` · `Riboswitch` · `SWIG` · `Sequence_alignment` · `Simulated_annealing` · `Small_RNA` · `Spliceosome` · `Stemloc` · `T-Coffee` · `Three_prime_untranslated_region` · `Very_large-scale_neighborhood_search` · [[Wayback_Machine]] > Summary stub · part of Systems Engineering · [Wikipedia source](https://en.wikipedia.org/wiki/List_of_RNA_structure_prediction_software) ## Summary This list enumerates software for RNA [[Structure|structure]] prediction, used to compute the secondary and tertiary folding of RNA molecules from their sequences. Because RNA structure governs function, such tools support research in molecular biology, drug design, and synthetic biology. They apply thermodynamic models, comparative methods, and increasingly [[Machine_learning|machine learning]]. The list catalogs the specialized programs and servers available for this task. ## Key points - Enumerates RNA structure prediction software - Predicts RNA secondary and tertiary structure - Uses thermodynamic, comparative, and ML methods - Supports molecular biology and drug design - Catalogs specialized programs and servers ## Relation to Systems Engineering RNA structure prediction tools are specialized analytical components, exemplifying the kind of domain software a systems approach integrates into workflows. ## Sources - [List of RNA structure prediction software — Wikipedia](https://en.wikipedia.org/wiki/List_of_RNA_structure_prediction_software) Back to Systems Engineering --- <!-- SEMIOTIC-PROFILE:START --> ## Semiotic profile > *The semiotic universals this article invokes, machine-derived from the crossref — **unverified** (born so). Populated 2026-07-06 for the Systems room.* **Universals (3):** 🟡 structure (8) · 🟡 system (6) · 🟡 sequence (1) **Enter by sign:** Systems Semiotic Gateway · Alphabetum · Icon Registry · ← Systems Portal <!-- SEMIOTIC-PROFILE:END --> ## Wikipedia : Wikitube **Strict pair:** [Wikipedia](https://en.wikipedia.org/wiki/List_of_RNA_structure_prediction_software) : [Wikitube](https://en.wikitube.io/wiki/List_of_RNA_structure_prediction_software) ## Previous hub tags Tree parent: [[Systems_engineering]]. Legacy hubs: none. --- *Sources: 1 legacy note. Minted wave 1, 2026-07-30 (v1.6 order).*