RNA Secondary Structure Energy Calculator

RNA molecules fold into shapes that determine their biological function — the RNA Secondary Structure Energy Calculator predicts how stable those shapes are by calculating the thermodynamic energy of folding. Enter your RNA sequence (A, U, G, C), select your calculation method (MFE, Partition Function, or both), and set your temperature and salt concentration to get the Minimum Free Energy of the most stable structure. Secondary outputs include Ensemble Free Energy, Ensemble Diversity, MFE Structure Frequency, and Thermodynamic Stability per nucleotide.

Enter single-stranded RNA sequence in 5' to 3' direction

Nucleic Acid Type *

°C

Temperature for energy parameter scaling

M

Monovalent salt concentration in molar

Prohibit GU wobble pairs at the end of helices

Prohibit isolated base pairs (lonely pairs)

Assume RNA molecule is circular

Include G-quadruplex structures in prediction

Results

Minimum Free Energy

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Ensemble Free Energy

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Ensemble Diversity

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MFE Structure Frequency

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Thermodynamic Stability

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Frequently Asked Questions

What is minimum free energy (MFE) in RNA structure prediction?

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

How does temperature affect RNA secondary structure energy?

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.

What is the difference between MFE and partition function calculations?

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.

Why should I avoid isolated base pairs in RNA folding?

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.

How does salt concentration affect RNA structure prediction?

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.

What are G-quadruplexes and when should I include them?

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.

What does ensemble diversity tell me about RNA structure?

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

Can I predict DNA secondary structures with this calculator?

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.