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 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.

apo–holo entries

PDB structures

unique ligands

functional types

Browse the Database Run a Query

5SWE adenine riboswitch, apo end of the morph

Riboswitch ▶ play morph 5SWE · ADE apo–holo Adenine riboswitch converted in crystal by ligand mixing · rmsd

HIV TAR ▶ play morph 2L8H · L8H apo–holo HIV-1 TAR 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 binding site, end to end

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

holo apo

RMSD (Å) Pocket RMSD (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.

Functional type (NAKB) · counts are binding pockets

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 binding site, end to end

A structurally diverse, redundancy-reduced RNA dataset

Everything you can do

Database gallery

Query your own

Multi-ligand pocket groups

Clustering & redundancy

Statistics