lamm-mit/pdb
skills/pdb/SKILL.md
3D protein structure search via RCSB PDB. Input MUST be a protein/gene name (e.g. 'KRAS', 'EGFR', 'BTK') or a 4-character PDB ID (e.g. '6OIM'). Returns zero results for drug/chemistry phrases such as 'covalent inhibitors' or 'warhead selectivity'. Strip all drug qualifiers and pass only the target protein name or PDB ID.
$ install --global
skillsauthnpx skillsauth add lamm-mit/scienceclaw pdbInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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Last scanned: Apr 6, 2026, 12:52 PM41.1s2 files scanned
SKILL.md
- name:
- pdb
- description:
- 3D protein structure search via RCSB PDB. Input MUST be a protein/gene name (e.g. 'KRAS', 'EGFR', 'BTK') or a 4-character PDB ID (e.g. '6OIM'). Returns zero results for drug/chemistry phrases such as 'covalent inhibitors' or 'warhead selectivity'. Strip all drug qualifiers and pass only the target protein name or PDB ID.
PDB - Protein Data Bank
Search and fetch protein structures from the RCSB Protein Data Bank.
Usage
Search for structures:
python3 {baseDir}/scripts/pdb_search.py --query "kinase human"
Get structure details:
python3 {baseDir}/scripts/pdb_search.py --pdb-id 1ATP
Search by sequence:
python3 {baseDir}/scripts/pdb_search.py --sequence "MTEYKLVVVGAGGVGKSALTIQLIQ" --identity 70
Parameters
| Parameter | Description | Default |
|-----------|-------------|---------|
| --query | Text search query | - |
| --pdb-id | Specific PDB ID to fetch | - |
| --sequence | Sequence for similarity search | - |
| --identity | Minimum sequence identity % | 90 |
| --max-results | Maximum results | 10 |
| --format | Output: summary, detailed, json | summary |
Examples
# Search for insulin structures
python3 {baseDir}/scripts/pdb_search.py --query "insulin"
# Get details for a specific structure
python3 {baseDir}/scripts/pdb_search.py --pdb-id 4HHB
# Find structures similar to a sequence
python3 {baseDir}/scripts/pdb_search.py --sequence "MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH" --identity 50
# Get JSON output
python3 {baseDir}/scripts/pdb_search.py --query "p53 DNA binding" --format json
Output Fields
- PDB ID - 4-character structure identifier
- Title - Structure title
- Resolution - X-ray resolution in Angstroms
- Method - Experimental method (X-RAY, NMR, EM)
- Release Date - When structure was released
- Organism - Source organism
- Chains - Polymer chains in structure
Query Limitations — Read Before Using
PDB stores experimentally determined 3D structures. Queries must target proteins or genes with known deposited structures. Abstract or chemistry-only queries return zero results.
| ❌ Fails | ✅ Works | |---|---| | "BTK covalent inhibitor" | "BTK" or "Bruton tyrosine kinase" | | "warhead optimization" | "1K2P" (direct PDB ID) | | "ADMET prediction" | "EGFR kinase inhibitor complex" |
Tips for avoiding zero results:
- Use short protein names or gene names:
"BTK","p53","EGFR" - Use a specific PDB ID (
--pdb-id 3K54) when you already have one from UniProt cross-refs - If zero results, broaden the query — e.g.,
"kinase"instead of"covalent kinase inhibitor BTK" - Not all proteins have PDB entries; check UniProt cross-refs first
Notes
- Uses RCSB PDB REST API (no authentication)
- Structures include X-ray, NMR, and cryo-EM
- Resolution shown for X-ray structures
- Links provided to 3D viewers
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