alphafold-structure-provenancelisted

Life sciences / Structural biology — Taxon-scoped UniProt accession lookup plus version-aware AlphaFold DB structure retrieval. Keeps pLDDT/PAE quality triage strictly separate from oligomer and complex assembly flags, and requires recording exactly which AlphaFold structure version any derived quantity (such as a HullRad diffusion coefficient) was computed from. Encodes AlphaFold DB version-retention behaviour: latestVersion is authoritative for what can be downloaded today, while allVersions is a historical list only — older version-numbered structure, PAE, and confidence files typically 404 once an entry moves to a newer version. WHEN: "look up UniProt accessions for an organism", "fetch AlphaFold structures", "AlphaFold API", "pLDDT triage", "PAE triage", "structure quality assessment", "AlphaFold model version", "latestVersion vs allVersions", "oligomer flag", "structure provenance", "AlphaFold DB 404".
timothymeyers/discovery-tools · ★ 1 · AI & Automation · score 70

Install: claude install-skill timothymeyers/discovery-tools

# alphafold-structure-provenance — Taxon-Scoped UniProt Lookup + Version-Aware AlphaFold Retrieval Hub skill for two chained steps that recur across structure-quality and hydrodynamic-property (e.g. HullRad) workflows: 1. **Taxon-scoped UniProt accession lookup** — resolve which UniProt accessions belong to a given organism/taxon before doing anything with AlphaFold. 2. **Version-aware AlphaFold DB structure retrieval** — fetch the *correct, currently-downloadable* structure/confidence/PAE files for those accessions, and record exactly which AlphaFold model version was used for every derived downstream quantity. It also documents two triage/flagging steps that must stay independent of each other and of the version-provenance step: **pLDDT/PAE quality triage** and **oligomer/complex assembly flags**. ## When to use Trigger this skill when the user asks to: - "Look up all UniProt accessions for organism/taxon X" or otherwise scope a protein list to a specific organism before structural analysis. - "Fetch AlphaFold structures for these accessions", "download AlphaFold models", or "get pLDDT/PAE for these proteins". - Debug an AlphaFold DB `404` on a structure/confidence/PAE file that used to work, or reconcile a mismatch between a locally-recorded model version and what AlphaFold DB currently serves. - Assess structure quality (pLDDT bands, low-confidence segments, PAE) for a candidate list. - Decide whether a monomer AlphaFold model is trustworthy