Link predicted models to experimental PDB counterparts

[CedricHermansBIT]

Adds UniProt-centred experimental counterpart discovery for predicted structures.

Workflow

• AlphaFold DB inputs retain their UniProt accession and query 3D-Beacons automatically;
• uploaded AF2/ColabFold, ESMFold and other predicted models can be looked up by a manually supplied UniProt accession;
• only PDBe records explicitly labelled EXPERIMENTALLY DETERMINED are shown;
• hits are ranked by mapped UniProt coverage, then resolution when available;
• selecting a hit loads the PDB entry directly into the existing Compare workflow, including chain selection, sequence alignment, wrapped phi/psi differences, Conformational Change Explorer and linked paired 3D inspection.

Interpretation safeguards

• same UniProt is treated as a discovery link, not proof of the same biological state;
• uploaded coordinates are not sent to 3D-Beacons; only the supplied UniProt accession is queried;
• no live external API dependency in CI: parser/filter tests use a mock response, while browser coverage checks UI/server validation without making the external request.

Tests and docs

• tests/counterparts.R covers provider/category filtering, PDB ID extraction, ranking, duplicates and no-hit responses;
• prediction-browser CI verifies counterpart controls and local accession validation;
• dedicated workflow/limitations documentation is included.