Structure-based function prediction

When does protein structure help GO review, and when does it not?

AI Gene Review · projects/STRUCTURE_FUNCTION · 2026

Bottom line

  • HMMs fail below ~20–30% identity, where fold and active sites often persist. We surveyed fold-, motif- and model-level tools and tested them on our own cases.
  • lanM: structure adds nothing (still "EF-hand, calcium"). DUF4246: Foldseek finds 2OG-Fe(II) oxygenases at 8–15% identity, matching Holm 2023.
  • Local catalytic-residue checks already decide calls (PqsC/PqsB, EryCII, cds1, PHYKPL). The planned pipeline script does not exist yet.

Three levels where structure can help

  • Global fold (SCOP/CATH/ECOD): "what kind of protein"; transfer safe only at superfamily level. TIM barrels span 5 of 6 EC classes.
  • Local motifs (M-CSA/EnzyMM, PARSE): catalytic geometry; the highest-value level. PARSE found 183 putative enzymes in 34,015 dark-proteome structures.
  • Learned models (SaProt, ProstT5, DPFunc, DeepGO-SE): 3Di-aware predictors, but trained on existing GO, so they inherit its errors.

Two cases, opposite answers

lanM in the review

The IEA calcium-binding row is KEEP_AS_NON_CORE: technically true (near-millimolar Ca²⁺) but not the physiological function (picomolar Ln³⁺).

Where structure pays off

Local active site beats global fold

Gene Fold Active site Call in review
PSEAE/pqsC FabH/KAS-III Cys-129/His-269 dyad condensing enzyme
PSEAE/pqsB FabH/KAS-III lacks the dyad non-catalytic partner
SACEN/eryCII P450 no heme cysteine pseudoenzyme
MYCTU, VIBCH/cds1 PLP, Cys-synthase family ASSGST, not PTSGNTG IBA L-cysteine biosynthetic process REMOVE
human/PHYKPL aminotransferase III phospho-lyase IEA transaminase activity REMOVE

Status and next steps

  • ✅ Tool landscape, lanM negative case, DUF4246 positive case, pipeline examples.
  • ⬜ Write scripts/structural_search.py (AlphaFold → Foldseek) and save runs.
  • ⬜ Foldseek and EnzyMM on cds1 (O69652) and PHYKPL (Q8IUZ5): do structural hits recover what IBA/IEA got wrong?
  • ⬜ Screen DUF-only proteins in the pipeline; treat hits as ISS-level leads.

Read more: projects/STRUCTURE_FUNCTION.md · genes/METEA/lanM/ · genes/MYCTU/cds1/