Confidence scores aren't assays: a guide to evaluating protein-structure AI claims
Fair-Rain3366 · reddit · 2026-09-07
A detailed guide argues AI protein-structure confidence scores cannot substitute for biological assays.
- A FASTA sequence doesn't fully specify a prediction job: single chains, assemblies, and protein-ligand complexes need different inputs and validation; database versions, alignments, templates, and sampling protocols all change what was tested.
- Confidence metrics likewise differ — local confidence, domain placement, and interface confidence measure distinct geometric aspects, and none measures catalytic activity or binding in a specific assay.
- More diffusion samples explore candidates but don't automatically form a thermodynamic ensemble.
The author proposes asking which biological claim an output actually supports, and what evidence is needed before carrying a model-selected structure into a downstream functional claim.
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