Launching STINGAllo — Quick Learn

Route 1 — a published PDB entry

Use this when the structure you care about is already in the Protein Data Bank. Predictions for published entries are pre-computed, so the result appears immediately.

Open the Server page
Go to Server. The first card is “Use a published PDB entry”.
Enter a four-character PDB code
Type it into the PDB Code field — for example 3I54. Four letters or digits. If you do not have one to hand, use one of the example codes offered beneath the field (3I54, 2IEG, 3PG9, 3UO9).
Press “Chains?”
STINGAllo looks the entry up at RCSB and lists every chain it contains, with the source organism, the molecule name, the UniProt accession, the EC number where one applies, and the sequence length. Use that to identify the chain you want.
Select exactly one chain
Click a chain in the list. It appears under Selected PDB chain. STINGAllo analyses one chain per run — if you select more than one, remove the extras with the × button before launching.
Press “Launch STINGAllo”
The result page opens with the predicted allosteric site-forming residues listed and drawn on the structure.

If nothing happens

The launch button reports inline when no chain, or more than one chain, is selected. A code that RCSB does not recognise returns no chains — check the four characters and try again.

Route 2 — your own structure

Use this for a structure that is not in the PDB: a model, a private structure, or a modified entry. This route runs the full descriptor pipeline, so it is not instant.

Choose a .pdb file
In the “Upload your own structure” card, pick a single coordinate file. STINGAllo reads its chains and offers them in the Chain menu.
Select the chain to analyse
Descriptors are computed for the chain you select plus one neighbouring chain, because several interface descriptors need inter-chain contacts.
Press “Launch STINGAllo” and wait
A progress bar and elapsed-time counter appear. Runs normally take several minutes. Keep the tab open — closing it cancels the run. The full pipeline log is available under Pipeline log if you want to follow it or report a problem.

Expect a wait

The upload route recalculates every descriptor from scratch. If the structure you need is already published, Route 1 returns the same prediction immediately.

What you get back

The residue list: Every predicted allosteric site-forming residue, as a three-letter residue name and its sequence number, with a plain-text copy for pasting into other tools.
The 3D view: The selected chain as a cartoon, with a Van der Waals surface drawn over the predicted residues. Cartoon colour, surface colour and surface opacity are adjustable, and residue labels can be toggled on.
A download bundle: A .zip containing the coordinates, a PyMOL script that reproduces the view, the residue list as text, and a 300 dpi image.
Programmatic access: The same prediction is available from the REST API for pipeline use.

Next: the interface reference, or the case study.