RNAcofold

What RNAcofold Does

RNAcofold predicts the joint secondary structure of two interacting RNA molecules. ProteinIQ returns the dimer MFE by default and supports partition-function ensemble metrics only when explicitly requested.

Inputs

• Provide two RNA sequences in FASTA or plain-sequence format.
• Optional Concentration table input enables concentration-dependent equilibrium calculations.

Settings

• Temperature, Disallow lonely pairs, and Dangling ends: standard ViennaRNA folding controls
• Compute partition function: opt in to ensemble metrics such as ensemble free energy, MFE frequency, ensemble diversity, centroid, MEA, and binding free energy
• Concentration table: optional native concentration mode input

Partition-function mode is off by default to preserve standard behavior.

Output

The standard structure row reports:

• interaction identifier
• sequence lengths
• dimer structure
• MFE
• optional ensemble metrics when partition-function mode is enabled

When concentration mode is enabled, additional concentration rows report:

• initial concentrations
• equilibrium concentrations for AA, BB, AB, A, and B
• native free-energy terms used for the equilibrium calculation