# A Graph Grammar for Modelling RNA Folding

@inproceedings{Mamuye2016AGG, title={A Graph Grammar for Modelling RNA Folding}, author={Adane Letta Mamuye and Emanuela Merelli and Luca Tesei}, booktitle={GaM@ETAPS}, year={2016} }

We propose a new approach for modelling the process of RNA folding as a graph transformation guided by the global value of free energy. Since the folding process evolves towards a configuration in which the free energy is minimal, the global behaviour resembles the one of a self-adaptive system. Each RNA configuration is a graph and the evolution of configurations is constrained by precise rules that can be described by a graph grammar.

## 5 Citations

### Qfold: a new modeling paradigm for the RNA folding problem

- BiologyJ. Heuristics
- 2021

A Quadratic Unconstrained Binary Optimization (QUBO) modeling paradigm that fits naturally with the parameters and constraints required for RNA folding prediction is presented.

### An algebraic language for RNA pseudoknots comparison

- Computer ScienceBMC Bioinformatics
- 2019

An algebraic language to represent RNA secondary structures with arbitrary pseudoknots is introduced and it is shown that the tree grammar with its operators permit to uniquely represent any RNA secondary structure as a tree.

### Process calculi may reveal the equivalence lying at the heart of RNA and proteins

- BiologyScientific Reports
- 2019

By applying Milner’s CCS process algebra to highlight the distinguishing features of the two folding processes, this work has discovered an abstraction level at which they show behavioural equivalences.

### Predicting 3D RNA Folding Patterns via Quadratic Binary Optimization

- BiologyArXiv
- 2021

Three dimensional RNA folding predictions are developed by adding penalty and reward parameters to a previous two dimensional approach based on Quadratic Unconstrained Binary Optimization (QUBO) models, which provides flexibility in the amount of three dimensional folding allowed.

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