Query · SMARTFlexDB

Analyze your own apo–holo pair

Upload a ligand-bound (holo) and a ligand-free (apo) structure of the same RNA and name the ligand. SMARTFlexDB runs the same structural analysis as for the curated pairs: binding site, sequence alignment, per-residue displacement, 3D superposition and morph, secondary structure and ligand–RNA interactions.

Each result is tagged by how it is produced:
tool-derived by an established tool (x3dna-dssr, US-align / Kabsch, RDKit)
geometry-derived computed from coordinates

Scope and limitations

We locate your ligand in the holo structure, superpose the apo onto it and compute every panel from your two files.

Computed from your coordinates. Binding site, displacement, contacts and base pairs come from DSSR and gemmi. The superposition is the site’s sequence-anchored Kabsch fit over the C3′ atoms of all binding-site chains at once; a one-chain fit also tries a US-align superposition and keeps the lower-RMSD of the two. The TM-score comes from US-align. tool-derived (x3dna-dssr, US-align / Kabsch)geometry-derived (gemmi distances)
Sequence cluster only. The result reports the nearest existing sequence cluster (MMseqs2, ≥ 70% identity over ≥ 80% of the released sequence, as on Clustering). It is an assignment, not a re-clustering. The structure and pocket axes are not assigned. tool-derived (MMseqs2)
The morph is interpolation, not MD. A straight-line interpolation between your two structures, a visualization only. geometry-derived