How do I install the Pdb skill?

Run npx skillmds@latest add lamm-mit/pdb in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

This skill has not completed SkillMD's automated safety review yet. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Pdb?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

lamm-mit (@lamm-mit) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Pdb by lamm-mit — Agent Skill

Name: Pdb
Author: lamm-mit

Pdb

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.

lamm-mit c4b0f7a 3 files · 31.5 KB Updated Sep 17, 2026

File contents

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

---name: pdbdescription: 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 BankSearch and fetch protein structures from the RCSB Protein Data Bank.## Usage### Search for structures:```bashpython3 {baseDir}/scripts/pdb_search.py --query "kinase human"```### Get structure details:```bashpython3 {baseDir}/scripts/pdb_search.py --pdb-id 1ATP```### Search by sequence:```bashpython3 {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```bash# Search for insulin structurespython3 {baseDir}/scripts/pdb_search.py --query "insulin"# Get details for a specific structurepython3 {baseDir}/scripts/pdb_search.py --pdb-id 4HHB# Find structures similar to a sequencepython3 {baseDir}/scripts/pdb_search.py --sequence "MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH" --identity 50# Get JSON outputpython3 {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 UsingPDB 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

Frequently asked questions

Pdb