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pdb-database
95 / 100 · Low risk
Fine to try.
By sharkrebel/everything-everywhere-for-antigravity (GitHub) · data · 89 stars · scanned at commit 71bf78c
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
- skills/pdb_database/SKILL.md, line 103
uv run scripts/search_pdb.py --query '{ "query": { "type": "terminal", "service": "sequence", "parameters": { "evalue_cutoff": 1, "identity_cutoff": 0.9, "seque - skills/pdb_database/SKILL.md, line 108
uv run scripts/search_pdb.py --query '{ "type": "terminal", "service": "structure", "parameters": { "value": {"entry_id": "6LU7", "asym_id": "A"}, "number_of_ca - skills/pdb_database/SKILL.md, line 113
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 - skills/pdb_database/SKILL.md, line 118
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 - skills/pdb_database/SKILL.md, line 128
uv run scripts/search_pdb.py --query '{ "type": "terminal", "service": "full_text", "parameters": { "value": "isopeptide + ( collagen | fibrinogen )" } }' --ret - skills/pdb_database/SKILL.md, line 142
uv run scripts/download_coordinate_files.py --ids "4HHB,6BEA" --format "mmcif" --output_dir <OUTPUT_DIR> - skills/pdb_database/SKILL.md, line 162
uv run scripts/fetch_pdb_metadata.py --query '{ entries(entry_ids: ["1STP", "2JEF", "1CDG"]) { rcsb_id struct { title } exptl { method } } }' --output results.j - skills/pdb_database/SKILL.md, line 167
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_ - skills/pdb_database/SKILL.md, line 172
uv run scripts/fetch_pdb_metadata.py --query '{ entries(entry_ids:["7NHM", "5L2G"]){ polymer_entities { rcsb_id rcsb_polymer_entity_container_identifiers { refe
Other copies in this repository
sharkrebel/everything-everywhere-for-antigravity has 1 more folder with a skill named pdb-database. This page shows the lowest-scoring copy.
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=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/sharkrebel/everything-everywhere-for-antigravity' "$d" && git -C "$d" checkout --quiet '71bf78cfb929edcf8972b707085c40cc0cf23bae' -- 'skills/pdb_database' && mkdir -p ~/.agents/skills && cp -R "$d"/'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 sharkrebel/everything-everywhere-for-antigravity shows the score of its lowest-scoring skill.
[](https://zalavijaysinh.github.io/skilltrust/repos/sharkrebel/everything-everywhere-for-antigravity/)
Score history
| Date | Version | Score |
|---|
| 2026-11-11 | 71bf78c | 95 |