Related tools
RNAdos
RNAdos calculates density-of-states summaries for RNA sequences, reporting representative structures and state counts across energy bands.
RNAeval
RNAeval calculates the free energy of an RNA secondary structure for a given sequence. Evaluates if a proposed structure is thermodynamically favorable.
RNAfold
RNAfold predicts RNA secondary structure using minimum free energy (MFE) algorithms and optionally returns partition-function ensemble metrics when explicitly enabled.
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.
IgGM
IgGM is a generative foundation model for antibody and nanobody design against a target antigen. Supports CDR design, affinity maturation, inverse design, and framework design. Requires an antigen structure (PDB) and antibody sequences with "X" marking positions to design.
RNAalifold
RNAalifold computes consensus RNA secondary structure from a multiple sequence alignment. Uses covariation information to improve prediction accuracy for evolutionarily conserved structures.
RNAcofold
RNAcofold predicts the joint secondary structure of two interacting RNA molecules and optionally reports partition-function and concentration-dependent equilibrium metrics.
What RNAinverse Does
RNAinverse performs inverse folding for a supplied target structure and starting sequence or alphabet constraint string. ProteinIQ wraps the upstream ViennaRNA CLI workflow instead of generating random starts inside the wrapper.
Inputs
- Provide one target structure in dot-bracket notation.
- Provide one starting sequence or alphabet constraint string.
Settings
Repeat: upstream repeat count. Default1.Final scoring mode: optional upstream final scoring selector.Alphabet: optional upstream alphabet constraint.Temperature,Dangling ends, andParameter file content: ViennaRNA model controls where supported.
Output
The results table reports one row per designed sequence:
- design number
- target structure
- starting sequence
- designed sequence
- Hamming distance
- optional structure distance
- optional target probability