UNAfold

UNAfold is a computational tool designed for predicting the secondary structure of RNA molecules. It operates by calculating the minimum free energy of possible RNA structures, considering base pairing and stacking interactions. The algorithm is based on dynamic programming, allowing it to efficiently explore the conformational space of an RNA sequence. UNAfold can predict not only the most stable structure but also a set of suboptimal structures, providing insights into the flexibility and potential alternative conformations of the RNA.

The program takes an RNA sequence as input and outputs a representation of the predicted secondary structure, often in the form of a dot-bracket notation or a graphical representation. It also provides thermodynamic parameters such as the minimum free energy. UNAfold is widely used in molecular biology research for tasks such as designing RNA molecules with specific functions, analyzing the impact of mutations on RNA stability, and understanding RNA-protein interactions. Its accuracy is influenced by the quality of the thermodynamic parameters used in its calculations and the inherent complexity of predicting biological structures. UNAfold is part of a suite of RNA bioinformatics tools.