How to read the results
RFoldSearch encodes every nucleotide as one of 80 learned 3Dr structural states, aligns the resulting token strings, and reports the closest structures in each database.
Input
Paste or upload one RNA chain as PDB or mmCIF (up to the size shown under the box). The first RNA chain in the file is used. Every nucleotide needs its C3′, C4′ and O4′ atoms; nucleotides without them are skipped, and chains shorter than 20 nucleotides cannot be searched.
1. Choose a mode
RFoldSearch (recommended for most searches) prefilters with a k-mer index, aligns structural tokens with affine-gap Smith–Waterman, superposes the aligned C4′ atoms, and ranks hits by the structure score SSW × TM-score. RFoldSearch-TM re-scores the same candidates with US-align on the coordinates, which improves the structural ranking at a higher cost.
2. The hit table
Click a column heading to sort by it, and a row to open the hit.
| Column | Meaning |
|---|---|
| Target | The matched chain: the PDB entry with its chain, or the RNAcentral id of a predicted model (it links to the entry page). |
| RNA / organism | The name of the RNA and its source organism. Predicted models also show their Rfam family when one is assigned. |
| pLDDT | Predicted databases only: the mean pLDDT of the model, a measure of its quality (higher is better, 100 is the maximum). |
| Seq identity | Nucleotide identity over the aligned positions. Databases without sequences show 3Dr identity instead: the fraction of aligned pairs with the same structural token. |
| RMSD (Å) | Root-mean-square deviation of the superposed aligned nucleotides. |
| Structure score | The ranking score, SSW × TM-score. A hit has to match locally and in the arrangement of its aligned segments. |
| TM-score | The TM-score of the token alignment after superposition, normalised by the query and by the target length and averaged. In RFoldSearch-TM it is the US-align TM-score of the two whole chains. |
| E-value | The expected number of unrelated hits at least this good by chance. It is calibrated for each query (its length and token composition) against the database it is searched in, and is computed from SSW, so it does not always increase down the list. Databases that have not been calibrated yet report no E-value. |
| Query cov, Target cov | The share of the query and of the target that the alignment spans. |
3. Inside a hit
Click a row to open it. Four numbers describe the alignment: the Aligned-region TM-score, the RMSD, the query and target coverage (with the aligned ranges underneath) and the sequence identity (with the 3Dr identity underneath; for databases without sequences only the 3Dr identity). The Aligned-region TM-score is the TM-score computed over the aligned nucleotides only, so it can differ from the TM-score in the table.
The 3Dr line
Between the query and target sequences, | marks the same structural token, + a positive Structure-BLOSUM substitution and . any other aligned pair. Positions count nucleotides with a complete C3′, C4′, O4′ backbone. Databases without sequences show the target residues as ·.
The 3D view
The query is orange and the hit is blue after superposition on the aligned nucleotides; pale colours are unaligned. Rotate and zoom with the mouse, and click a nucleotide, in the 3D view or in the alignment, to see which nucleotide of the other structure it is aligned to. Clicking in the alignment also centres the 3D view on it.
4. Databases
PDB-RNA (all RCSB RNA chains) and RNAsolo 2.0 (a non-redundant representative set) hold experimental structures. NuFold holds predicted structures, which carry no sequence, so 3Dr identity is the main measure of agreement there.
