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pdb-database
95 / 100 · Low risk
Fine to try.
By franklee16/academic-research-skills (GitHub) · data · 234 stars · scanned at commit 9a4b2db
Use when you want to search for or download experimentally-determined 3D structures for biomolecules (proteins, nucleic acids, bound ligands). Supports searching by sequence similarity, structure similarity, chemical and other attributes. Also use to get metadata about biomolecular structure experiments.
Works with any agent that supports SKILL.md skills.
What this skill can do
Runs commands on your computer
The author does not mention this.
Found in 12 places.
Show 9 more
- science-skills/pdb_database/SKILL.md, line 99
uv run scripts/search_pdb.py --query '{ "query": { "type": "terminal", "service": "sequence", "parameters": { "evalue_cutoff": 1, "identity_cutoff": 0.9, "seque - science-skills/pdb_database/SKILL.md, line 104
uv run scripts/search_pdb.py --query '{ "type": "terminal", "service": "structure", "parameters": { "value": {"entry_id": "6LU7", "asym_id": "A"}, "number_of_ca - science-skills/pdb_database/SKILL.md, line 109
uv run scripts/search_pdb.py --query '{ "type": "terminal", "service": "seqmotif", "parameters": { "value": "C-x(2,4)-C-x(3)-[LIVMFYWC]-x(8)-H-x(3,5)-H.", "patt - science-skills/pdb_database/SKILL.md, line 114
uv run scripts/search_pdb.py --query '{ "type": "terminal", "service": "chemical", "parameters": { "value": "InChI=1S/C8H9NO2/c1-6(10)9-7-2-4-8(11)5-3-7/h2-5,11 - science-skills/pdb_database/SKILL.md, line 124
uv run scripts/search_pdb.py --query '{ "type": "terminal", "service": "full_text", "parameters": { "value": "isopeptide + ( collagen | fibrinogen )" } }' --ret - science-skills/pdb_database/SKILL.md, line 138
uv run scripts/download_coordinate_files.py --ids "4HHB,6BEA" --format "mmcif" --output_dir <OUTPUT_DIR> - science-skills/pdb_database/SKILL.md, line 158
uv run scripts/fetch_pdb_metadata.py --query '{ entries(entry_ids: ["1STP", "2JEF", "1CDG"]) { rcsb_id struct { title } exptl { method } } }' --output results.j - science-skills/pdb_database/SKILL.md, line 163
uv run scripts/fetch_pdb_metadata.py --query '{ polymer_entities(entity_ids:["2CPK_1","3WHM_1","2D5Z_1"]) { rcsb_id rcsb_entity_source_organism { ncbi_taxonomy_ - science-skills/pdb_database/SKILL.md, line 168
uv run scripts/fetch_pdb_metadata.py --query '{ entries(entry_ids:["7NHM", "5L2G"]){ polymer_entities { rcsb_id rcsb_polymer_entity_container_identifiers { refe
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=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/franklee16/academic-research-skills' "$d" && git -C "$d" checkout --quiet '9a4b2db21fc4b217136ae4a0e6faad42d179ca03' -- 'science-skills/pdb_database' && mkdir -p ~/.agents/skills && cp -R "$d"/'science-skills/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 franklee16/academic-research-skills shows the score of its lowest-scoring skill.
[](https://zalavijaysinh.github.io/skilltrust/repos/franklee16/academic-research-skills/)
Score history
| Date | Version | Score |
|---|
| 2026-11-07 | 9a4b2db | 95 |