RNA Secondary Structure Energy Calculator

MFE is the secondary structure with the lowest thermodynamic energy, representing the most thermodynamically stable conformation of the RNA molecule at equilibrium.

Higher temperatures reduce base pairing stability and increase the entropy component of free energy. The energy parameters are rescaled based on temperature to predict structures at non-standard conditions.

MFE predicts the single most stable structure, while partition function calculates the ensemble of all possible structures weighted by their probabilities, providing ensemble diversity and base pairing probabilities.

Isolated base pairs (lonely pairs) are thermodynamically unstable and rarely observed in real RNA structures. Excluding them often improves prediction accuracy for biologically relevant structures.

Higher salt concentrations stabilize RNA structures by screening electrostatic repulsion between phosphate groups. This affects the energy calculations and can change the predicted optimal structure.

G-quadruplexes are four-stranded structures formed by guanine-rich sequences. Include this option when analyzing sequences with multiple G-tracts that might form these alternative structures.

Ensemble diversity measures how well-defined the secondary structure is. Low diversity indicates a single dominant structure, while high diversity suggests multiple competing conformations.

Yes, you can select DNA as the nucleic acid type. The calculator will use DNA-specific energy parameters (with thymine instead of uracil) for accurate DNA structure prediction.