SMARTFlexDB is a curated database of matched ligand-free (apo) and ligand-bound (holo) RNA structures. The current release contains apo–holo entries; each entry compares one holo PDB structure with one apo PDB structure and may cover one or more binding pockets. The release spans holo and apo PDB structures, ligands and functional types.
Each record includes aligned 3D structures, a 2D secondary-structure comparison, an interpolated apo→holo morph, sequence alignments, pocket-level measurements, and ligand–RNA interaction data.
SMARTFlexDB matches a ligand-bound binding site (holo) to a ligand-free structure of the same RNA (apo) and superposes them with a single rigid transform fitted over every chain of that binding site at once wherever those chains have a counterpart in the apo, so no strand is the reference. It then measures what moved — whole-chain RMSD, the binding-site RMSD, each chain's own shift, and how closely the two sequences agree. This card is one such binding pocket, read live from the API exactly as the pair page reads it; its holo structure may hold further binding pockets, which the pair page’s Binding pocket selector switches between.
Open this pair·
SMARTFlexDB provides sequence-, structure-, and pocket-level cluster assignments to support redundancy-aware dataset splits. Each map shows the relevant sequence, RNA chain, or binding pocket colored by cluster. See Clustering for thresholds, definitions, and limitations.
Functional type (NAKB) · counts are binding pockets
each point = one binding pocket · color = redundancy cluster
Browse & filter all apo–holo entries by functional type, ligand, motif, Δ and identity.
Browse allUpload an apo and holo CIF and a ligand code; run SMARTFlexDB's core structural analysis on demand.
OpenOne RNA pocket bound by a whole family of ligands — compare structural differences across the bound ligands.
OpenSequence / structure / pocket clusters + t-SNE for redundancy-controlled ML splits; export CSV.
OpenDistributions of conformational change, RNA length, ligand chemistry and method across the set.
Open