Related tools
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RNAdos calculates density-of-states summaries for RNA sequences, reporting representative structures and state counts across energy bands.
RNAeval
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RNALfold
RNALfold reports locally stable RNA secondary structures within a sliding window and returns their start and end positions on the input sequence.
RNAplfold
RNAplfold computes local base pair probabilities using a sliding window approach. Useful for analyzing accessibility and identifying binding sites in long RNA sequences.
RNAsubopt
RNAsubopt enumerates all RNA secondary structures within a specified energy range above the minimum free energy (MFE). Useful for exploring the structural ensemble and identifying alternative conformations.
ViennaRNA
ViennaRNA exposes a curated set of upstream-faithful ViennaRNA 2.7.2 workflows for RNA folding, density-of-states analysis, interaction prediction, local accessibility, plotting, inverse folding, and structure analysis.
RNAcofold
RNAcofold predicts the joint secondary structure of two interacting RNA molecules and optionally reports partition-function and concentration-dependent equilibrium metrics.
RNAdistance
RNAdistance compares RNA secondary structures using the selected upstream ViennaRNA distance representation and comparison mode.
RNAduplex
RNAduplex computes the hybridization structure between two RNA sequences. Predicts the optimal duplex formation and binding energy.
RNAplex
RNAplex predicts fast query-target RNA interactions, reporting parsed hit coordinates, structures, and energies.
What RNAfold Does
RNAfold predicts the minimum free energy structure for an RNA sequence. ProteinIQ wraps ViennaRNA RNAfold semantics by returning the MFE structure by default and exposing partition-function ensemble metrics only when Compute partition function is enabled.
Inputs
- Provide one or more RNA sequences in FASTA or plain-sequence format.
Settings
Temperature,Disallow lonely pairs,Circular RNA, andDangling ends: standard ViennaRNA folding controlsCompute partition function: opt in to ensemble metrics such as ensemble free energy, MFE frequency, ensemble diversity, centroid, and MEA outputs
Partition-function mode is off by default to preserve upstream behavior.
Output
Without partition function mode, the results table reports:
- sequence identifier
- sequence length
- MFE structure
- MFE
With partition function mode enabled, the table also reports:
- ensemble free energy
- MFE frequency
- ensemble diversity
- centroid structure, distance, and energy
- MEA structure, score, and energy
The Files tab contains structure plot files generated from the MFE structure.