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pdb-database
77 / 100 · Review before installing
Check before installing. Some of what it can do is expected: a coding skill usually runs build and test commands.
By jaechang-hits/SciAgent-Skills (GitHub) · coding · 388 stars · scanned at commit 65d6ceb
Query RCSB PDB (200K+ structures) via the public REST + GraphQL APIs with plain `requests` (no SDK). Search by text, attribute, sequence, or 3D structure similarity (Search API); retrieve metadata via GraphQL (Data API); download PDB/mmCIF from files.rcsb.org. For AlphaFold predictions use alphafold-database-access; for protein sequences only use uniprot-protein-database.
Works with any agent that supports SKILL.md skills.
What this skill can do
Downloads and installs other software
The author does not mention this.
Found in 2 places.
Runs commands on your computer
This is disclosed by the author in the skill's SKILL.md or README. Expected for a coding skill.
Found in 1 place.
Sends data to these websites: www.rcsb.org, files.rcsb.org
The author does not mention this.
Found in 23 places.
Show 17 more
- skills/structural-biology-drug-discovery/pdb-database/SKILL.md, line 135
r = requests.post(SEARCH, json=payload, timeout=30) - skills/structural-biology-drug-discovery/pdb-database/SKILL.md, line 182
r = requests.post(SEARCH, json=payload, timeout=30) - skills/structural-biology-drug-discovery/pdb-database/SKILL.md, line 209
r = requests.post(SEARCH, json=payload, timeout=30) - skills/structural-biology-drug-discovery/pdb-database/SKILL.md, line 232
r = requests.post(DATA, json={"query": gql}, timeout=30) - skills/structural-biology-drug-discovery/pdb-database/SKILL.md, line 247
r = requests.post(DATA, json={"query": gql}, timeout=30) - skills/structural-biology-drug-discovery/pdb-database/SKILL.md, line 262
r = requests.post(DATA, json={"query": gql}, timeout=30) - skills/structural-biology-drug-discovery/pdb-database/SKILL.md, line 278
r = requests.get(url, timeout=60) - skills/structural-biology-drug-discovery/pdb-database/SKILL.md, line 295
r = requests.get("https://www.rcsb.org/fasta/entry/4HHB", timeout=30) - skills/structural-biology-drug-discovery/pdb-database/SKILL.md, line 356
r = requests.post(SEARCH, json=payload, timeout=30) - skills/structural-biology-drug-discovery/pdb-database/SKILL.md, line 374
r = requests.post(SEARCH, json=payload, timeout=30) - skills/structural-biology-drug-discovery/pdb-database/SKILL.md, line 413
r = requests.post(DATA, json={"query": gql}, timeout=60) - skills/structural-biology-drug-discovery/pdb-database/SKILL.md, line 517
r = requests.post(SEARCH, json=payload, timeout=30) - skills/structural-biology-drug-discovery/pdb-database/SKILL.md, line 529
r2 = requests.post(DATA, json={"query": gql}, timeout=60) - skills/structural-biology-drug-discovery/pdb-database/SKILL.md, line 562
r = requests.post(SEARCH, json=payload, timeout=30) - skills/structural-biology-drug-discovery/pdb-database/SKILL.md, line 577
r2 = requests.post(DATA, json={"query": gql}, timeout=60) - skills/structural-biology-drug-discovery/pdb-database/SKILL.md, line 594
r = requests.get(f"https://files.rcsb.org/download/{pdb_id}.cif", timeout=60) - skills/structural-biology-drug-discovery/pdb-database/SKILL.md, line 644
r = requests.get("https://www.rcsb.org/fasta/entry/4HHB", timeout=30)
and 3 more places
Safer alternatives
Low-risk skills in the same category (coding) that look related. Check that one does what you need.
Install
Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.
if [ -e ~/.agents/skills/'pdb-database' ] || [ -L ~/.agents/skills/'pdb-database' ]; then echo 'A skill folder named pdb-database already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/jaechang-hits/SciAgent-Skills' "$d" && git -C "$d" checkout --quiet '65d6ceb875e20b751ffb3a6d8ee19516558789e1' -- 'skills/structural-biology-drug-discovery/pdb-database' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/structural-biology-drug-discovery/pdb-database' ~/.agents/skills/'pdb-database' && rm -rf "$d"; fi
Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'pdb-database' ~/.claude/skills/'pdb-database' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.
Badge for your README
The badge for jaechang-hits/SciAgent-Skills shows the score of its lowest-scoring skill.
[](https://zalavijaysinh.github.io/skilltrust/repos/jaechang-hits/SciAgent-Skills/)
Score history
| Date | Version | Score |
|---|
| 2026-11-07 | 65d6ceb | 100 |