Protein Structures — AlphaFold & PDB
Obtain and predict protein 3D structures — fetch AlphaFold predicted models from the AlphaFold DB, experimental structures from the RCSB PDB, or predict a novel sequence with ColabFold — and visualise them in the Mol* LiveView.
npx skills add BioTender-max/awesome-bio-agent-skills --skill structural_biology --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Protein Structures — AlphaFold & PDB How to get a protein's 3D structure and show it to the user. Most "predict the structure of protein X" requests do **not** require running AlphaFold — the AlphaFold DB already holds a precomputed prediction for nearly every known protein. Run a prediction only for a sequence that is not a known UniProt entry. ## 1. AlphaFold DB — predicted structures (the usual path) The AlphaFold Database has precomputed AlphaFold models for ~200M+ UniProt proteins. If the protein is a known UniProt entry, its predicted structure already exists — just fetch it (instant, free). **Use the API — do not hand-build file URLs** (the model version, currently `v6`, changes; the API always returns the live URLs): ```python import requests acc = "P00533" # UniProt accession (human EGFR) meta = requests.get( f"https://alphafold.ebi.ac.uk/api/prediction/{acc}", timeout=30 ).json()[0] cif_url = meta["cifUrl"] # also: pdbUrl, bcifUrl with open(f"{acc}.cif", "wb") as fh: fh.write(requests.get(cif_url, timeout=60).content) ``` **No UniProt accession yet?** Resolve a gene name / protein name to an accession first via the UniProt REST API (`https://rest.uniprot.org/uniprotkb/s
- 1. AlphaFold DB — predicted structures (the usual path)
- 2. RCSB PDB — experimental structures
- 3. Predicting a novel sequence
- ESMFold API — the practical path (no GPU)
- ColabFold / local AlphaFold — only with a real GPU
- Confidence — pLDDT
- Visualising the structure
What does the Protein Structures — AlphaFold & PDB skill do?
Obtain and predict protein 3D structures — fetch AlphaFold predicted models from the AlphaFold DB, experimental structures from the RCSB PDB, or predict a novel sequence with ColabFold — and visualise them in the Mol* LiveView.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill structural_biology --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 144 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.