Help · SMARTFlexDB

Help & getting started

SMARTFlexDB pairs ligand-bound (holo) RNA structures with ligand-free (apo) structures of the same RNA, so you can see how the binding pocket changes. The three steps below get you to a comparison; About explains the methods.

Getting started

Browse the Database. Each card is one entry: one holo structure paired with one apo structure (a holo structure with several apo structures has one entry for each).
- Filter with the facets on the left (identity, composition, functional type, method, pocket motif, ligand molecular weight, RNA length) or search by PDB ID, ligand or title. The page opens on the whole release; Reset filters brings it back.
- To find large or small changes, Sort by TM-score or RMSD, or click a bar on Statistics.
- Table lists one row per entry; CSV downloads a ZIP with those rows and the pocket-level comparisons that meet the filters.
Apo-Holo Relationship (the toolbar button next to Entry) shows one card per holo PDB structure, with its number of apo structures and of related holo structures (those sharing an apo structure). Click a card for a panel listing both, always over the whole release; click an apo structure to open that entry, or View to move to a related holo structure. The Local and Global identity facets apply to the Entries view only. This view sorts by RNA length, pocket size, ligand or PDB ID: TM-score and RMSD belong to one entry.
Open a pair. Click an entry card, or the holo PDB ID in a table row. The pair page shows the 3D superposition and the apo→holo morph (an entry without a morph says so), both 2D structures, the sequence alignment, per-residue displacement, base-pair changes, ligand–RNA interactions and downloads. If the holo structure has several binding pockets, pick one in the Binding Pocket menu next to the title.
Go deeper. Clustering: sequence, structure and pocket clusters for redundancy-aware train/test splits. Multi-ligand pocket groups: one RNA pocket bound by different ligands. Query: the same core analysis on your own apo and holo structures.

Interpretation note: Observed apo–holo conformational differences should not automatically be interpreted as resulting from ligand binding, as they may also reflect intrinsic RNA conformational heterogeneity or experimental context. Please interpret individual comparisons cautiously and on a case-by-case basis.

Try an example query

Each chip opens the Database with that filter applied.

SAM riboswitch Riboswitches Protein synthesis Viral RNA Aptamers Junction binding sites Internal-loop pockets X-ray structures

Frequently asked questions

What is an apo–holo entry?

One holo structure (RNA bound to a small-molecule ligand) paired with one ligand-free apo structure of the same RNA. Main rules (full list on About):

≥90% sequence identity (BLASTN) over ≥90% of both chains;
the same base at every binding-site residue (within 8 Å of the ligand);
no protein or DNA in either structure.

A holo structure paired with several apo structures has one entry for each; all count the same.

What do 1,187, 734, 266 and 434 mean?

Four ways of counting the same release:

Count	Unit	Where you see it
734	entries — one holo structure paired with one apo structure	Database Entry cards; table rows and the entry-level CSV in either view; Statistics charts of apo→holo change and identity
266	holo structures — one holo PDB structure, with all its binding pockets and ligands	Database Apo-Holo Relationship cards; Statistics charts of holo properties; the Clustering map
434	binding pockets — one ligand bound at one site of a holo structure	the pair page’s Binding Pocket menu; `GET /api/pairs`
1,187	pocket-level comparisons — one binding pocket against one apo structure; also the rows of the release file	the Full release file `smartflexdb_pairs.tsv` and the pocket-level CSV of a Database download; Statistics distributions

Entries. A holo structure is paired with 1 to 22 apo structures (7QSH and 7QP2 with 22), 186 distinct apo structures in all. A further 23 (holo, apo) pairings fail our sequence check (a binding-site chain has no matching apo chain, a binding-site base differs, or the apo has a different number of RNA strands); they are not shown and are not in the release file.
Holo structures. 46 bind more than one ligand, and their cards list them all (1O9M: 42B, BDG, P24, PA2); 150 distinct ligands in all. 101 hold more than one binding pocket.
Binding pockets. Identified by holo PDB, ligand, and the ligand’s chain and residue number, so one holo structure can hold several, even of one ligand (2ET5 has four RIO pockets). Each is measured on its own coordinates.
Release rows. The file has one row per binding pocket and apo structure, so every binding pocket appears with its own ligand, pocket RMSD, binding-site size, hydrogen bonds and motifs. Global RMSD, TM-score and the other whole-structure values depend on the apo structure and on the RNA strand the ligand sits on, not on the ligand, so binding pockets on one strand share them: 5XZ1 against 2FQN has a global RMSD of 2.89 Å on strand A, 2.65 on B and 2.67 on C, and the holo_chain column says which strand a row measures. Columns are described on the API page.

How is sequence identity defined?

Each entry has two, both comparing the holo RNA with the apo RNA:

Local identity	BLASTN identity (Altschul et al., 1990) inside the aligned region only, so unmatched ends are left out. Every entry has ≥90%.
Global identity	Needleman–Wunsch alignment (1970) of the full declared (SEQRES) sequences: every mismatch and gap counts, overhanging ends included. Unmodeled residues do not lower it. Rounded to whole percent, so 100 means ≥99.5%.

For a binding site on several chains, the published value is the ligand’s own chain’s (the chain the PDB entry assigns the ligand to), shown beside that chain’s alignment on the pair page.

Which chain is the superposition fitted on?

On all RNA chains of the binding site together (each chain with an atom within 8 Å of the ligand); no chain is the reference. Residues are paired by sequence alignment, each holo chain with its own apo chain, and the one rigid transform that minimises the C3′ RMSD over them (Kabsch, 1976) is applied to the whole apo structure. If a multi-chain binding site is fitted on the ligand’s own chain alone, the pair page says so and why.

For a multi-chain site the pair page gives each chain two RMSDs: in frame (in the shared superposition) and alone (fitted on its own, never larger). A large gap means the chains moved relative to each other.

Is the morph a molecular-dynamics trajectory?

No. It is a straight-line interpolation between the two superposed experimental structures, for visualization only. Playback slows near the two ends so they stay readable; that is a display choice with no kinetic meaning.

How do I download the data?

Your selection: CSV on the Database toolbar, a ZIP of two files: one row per entry, and one row per pocket-level comparison that meets the filters.
The whole release: smartflexdb_pairs.tsv and its .meta.json on the API page.
One entry: Download pair (ZIP) on its pair page, or single files in that page’s Downloads section.
Clusters: the CSV on Clustering.
From code: the REST API.

Contact & feedback

Questions, bug reports, corrections, or an apo–holo pair we missed? Email yanjun.li@ufl.edu and jiang.shiyu@ufl.edu. We respond to data corrections promptly. To analyze your own apo and holo structures, use Query.

License & data sources

The SMARTFlexDB derived data (pair list, descriptors, alignments) are released under CC-BY-4.0. Atomic coordinates come from the RCSB PDB and remain under its terms.