SMARTFlexDB

SMARTFlexDB

RNA · apo–holo · structural comparison

Explore structural differences between ligand-free and ligand-bound RNA pockets

SMARTFlexDB is a curated database of matched ligand-free (apo) and ligand-bound (holo) RNA structures. The current release contains unique RNA–ligand entries, represented by default pocket-level comparisons and comparisons to alternative apo structures ( comparisons in total). These records span PDB structures, ligands, and RNA functional classes.

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.

apo–holo comparisons

PDB structures

unique ligands

RNA classes

Browse the Database Run a Query

Riboswitch ▶ play morph 2HOO · BFT apo–holo TPP riboswitch with benfotiamine bound · rmsd

Viral RNA ▶ play morph 2L8H · L8H apo–holo viral RNA structural difference · vs apo · rmsd

Every pair includes Superposed apo and holo structures Interpolated apo–holo morph 2D secondary-structure diagrams Ligand–RNA contacts Local and global sequence identity

What a pair looks like

One entry, end to end

An entry matches one ligand-bound binding site (holo) to a ligand-free structure of the same RNA (apo) and superposes them. It then measures what moved — whole-chain RMSD, the binding-site RMSD, the largest single-residue shift, and how closely the two sequences agree. This one is read live from the API, exactly as the pair page reads it.

Open this pair

holo apo

RMSD (Å) Pocket RMSD (Å) Max Δ (Å) Global identity (%)

See the full comparison

A structurally diverse, redundancy-reduced RNA dataset

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.

RNA type (NAKB) · counts are apo–holo pairs

Open the Clustering map → download cluster assignments (CSV)

each point = one binding pocket · color = redundancy cluster

SMARTFlexDB

Explore structural differences between ligand-free and ligand-bound RNA pockets

One entry, end to end

A structurally diverse, redundancy-reduced RNA dataset

Everything you can do

Database gallery

Query your own

Pocket series

Clustering & redundancy

Statistics