Individual skill
alphafold-db
Access over 200M protein structures from AlphaFold DB; use when you need to retrieve predicted 3D structures (PDB/mmCIF), confidence metrics (pLDDT/PAE), or protein metadata by UniProt accession.
scientific-skills/Evidence Insight/alphafold-db/SKILL.md
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- bioinformatics Repository topic
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SKILL.mdcore · 2,424 bytesSKILL.mdcore · 2,424 bytesSKILL.mdcore · 2,424 bytesalphafold-db_audit_result_v1.jsonasset · 11,495 bytesout/P00520.cifasset · 1,026,470 bytesout/P00520.pdbasset · 708,749 bytesout/P00520_metadata.jsonasset · 515 bytesreferences/api_reference.mddoc · 1,446 bytesscripts/fetch_structure.pyruns · 3,142 bytes
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> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)
# AlphaFold Database Skill
## When to Use
- You have a UniProt accession (e.g., `P00520`) and need to download its AlphaFold-predicted 3D structure in **mmCIF** or **PDB** format.
- You want to assess prediction reliability using **per-residue pLDDT** confidence scores.
- You need **PAE (Predicted Aligned Error)** data to support domain-level interpretation or inter-domain confidence checks.
- You want to programmatically retrieve AlphaFold DB **metadata** (e.g., model/structure URLs and related fields) for downstream pipelines.
- You are building an automated workflow that fetches structures + confidence metrics for many proteins by UniProt ID.
## Key Features
- Fetch AlphaFold DB predicted structures by **UniProt accession**.
- Download structure files in **mmCIF (default)** or **PDB**.
- Retrieve and save **metadata JSON**, including confidence-related fields (e.g., pLDDT) and URL information.