# Example binder complexes

Checked 2026-10-07 against the local Hotspot/Binder Atlas (`hotspot_db/data/atlas.sqlite`,
read only) and the official Bindome target-metrics API. These are examples for
visualizing supplied poses, not a ranking of binder performance.

| Topology example | Bundled complex | Evidence |
| --- | --- | --- |
| Type I · EGFR (P00533) | Cetuximab Fab, [1YY9](https://www.rcsb.org/structure/1YY9) | Experimental source complex |
| Type II · TFRC (P02786) | None | No Bindome candidate or target–binder coordinate complex in the checked Atlas snapshot |
| Type III · SYT1 (P21579) | None | Atlas 8B8I contains only 17 target residues, below the app's existing 20-identical-Cα minimum |
| Type IV · CYB5A (P00167) | Bindome candidate | Computational, untested |
| Multi-pass, N out · ADRB2 (P07550) | Fab, [2R4R](https://www.rcsb.org/structure/2R4R) | Experimental source complex |
| Multi-pass, N in · ABCB1 (P08183) | MRK16 Fab, [7A65](https://www.rcsb.org/structure/7A65) | Experimental source complex |
| β-barrel · VDAC1 (P21796) | None | No Bindome candidate or binder complex in the checked Atlas snapshot |
| GPI · CD59 (P13987) | Bindome candidate | Computational, untested |
| Peripheral · PTGS2 (P35354) | None | No Bindome candidate or binder complex in the checked Atlas snapshot |

The live Bindome API returned 49 candidates for CYB5A, six for CD59 and empty
responses for the other seven accessions. One candidate per covered target was
selected as the first model returned by the API. The absence of a bundled example
does not establish that no binder exists elsewhere.

`manifest.json` records the exact source model identifiers, URLs, original and
bundled file hashes, author chain choices, extraction method, coverage checks and
alignment measurements against the frozen full target structures in
`benchmark/cache/examples-2026-10-07/`, using residues 26–102 for the mature CD59
example. Bindome files are unchanged. The PDB files
are mmCIF exports of the selected target and Fab author chains from the source's
parsed model, retaining coordinates and residue identifiers. Other chains are not
implicitly treated as binders. No source structure is pre-aligned to the receptor.

The button uses the existing alignment and binder-pose display/export paths. Its
current input is checked by sequence; source coordinates never replace the receptor.
Fits now use the source binding neighbourhood; the initial whole-fragment RMSD is
recorded separately. The manifest includes retained source contacts and severe
heavy-atom overlaps after transfer. CYB5A, ADRB2 and ABCB1 retain severe overlaps on
their frozen full receptor models; they are examples for inspecting an incompatible
transfer, not accepted poses. The viewer flags these overlaps and offers the original
complex as a separate, unchanged reference. Correction only carries a rigid binding
region; it cannot silently re-fit a deformed interface. The experimental status applies to the deposited complex,
not to a pose transferred to a different full-length or corrected receptor model.
Geometry checks do not establish binding activity.

## Opening the app directly from disk

Keep this `examples/binders` directory beside the app HTML, preserving the folder
structure. Each checked CIF also has a `.cif.js` text wrapper so the example button
works when the HTML is opened with `file://`: browsers permit local scripts but
block fetching neighbouring CIF files. The local web app loads the CIF directly.
Both paths validate the same original-text checksum before alignment and require
no download from Bindome or RCSB while these bundled files are present.

Regenerate wrappers after an intentional CIF/manifest update with
`python3 examples/binders/build_file_bundles.py` from the project directory.
The generator checks the manifest hash and packages text verbatim; it does not
download, parse, modify or pre-align coordinates. The `.cif.js` wrappers retain the
same licences and provenance as their CIF files. Copy the whole examples directory
when distributing the app with its optional examples.

## Attribution and licences

Bindome data are [CC BY 4.0](https://bindome.epfl.ch/static/index.html).
Credit: Wenckstern, Diaz-Rovira et al., *The Human Bindome: A Proteome-Scale Atlas of
Designed Binder Candidates*, bioRxiv (2026),
[doi:10.64898/2026.07.30.741542](https://doi.org/10.64898/2026.07.30.741542).
Individual model identifiers and metrics are in the manifest. These candidates
have not been experimentally validated.

PDB coordinates are provided under
[CC0 1.0](https://www.wwpdb.org/about/usage-policies). Credit the deposition authors
and primary papers linked from the corresponding RCSB entry pages above. Their
source identifiers and URLs remain in the app and exported alignment provenance.

The source Atlas database is not modified or required at app runtime. Local HTTP
loads use the bundled files. Direct `file://` use falls back to the original public
source downloads; a failure or changed source hash is reported without replacing
an existing manually supplied complex.

Validation: `tests/binder-examples-browser.cjs` exercises all five candidates with
real 3Dmol, matching chains, unchanged target coordinates and record, visibility,
placement where available, exports, missing examples, failed downloads and stale
input protection. Existing manual-complex tests remain in
`tests/binder-alignment-browser.cjs`.