Pdb Database
Access and query Jackspace's PDB protein structure database directly through this AI agent for research insights.
Install on your platform
We auto-selected Claude Code based on this skill’s supported platforms.
Run in terminal (recommended)
claude mcp add jackspace-pdb-database npx -- -y @trustedskills/jackspace-pdb-database
Or manually add to ~/.claude/settings.json
{
"mcpServers": {
"jackspace-pdb-database": {
"command": "npx",
"args": [
"-y",
"@trustedskills/jackspace-pdb-database"
]
}
}
}Requires Claude Code (claude CLI). Run claude --version to verify your install.
About This Skill
What it does
This skill, jackspace-pdb-database, allows AI agents to interact with a PDB (Protein Data Bank) database. It enables retrieval of protein structure data, including atomic coordinates and experimental details. The agent can query the database based on various criteria like PDB ID or keywords related to the protein.
When to use it
- Scientific Research: An AI agent needs to gather information about a specific protein for research purposes.
- Drug Discovery: Retrieve structural data of target proteins to aid in drug design and analysis.
- Educational Purposes: A student or educator wants to explore protein structures and learn about their properties.
- Bioinformatics Analysis: An agent needs to process and analyze a large dataset of protein structures.
Key capabilities
- Query PDB database by ID
- Retrieve atomic coordinates
- Access experimental details for proteins
- Search using keywords related to the protein
Example prompts
- "Get me the structure data for PDB ID 1AKE."
- "Find all proteins with 'kinase' in their description."
- “What are the experimental conditions used to determine the structure of 4HHB?”
Tips & gotchas
The skill relies on a stable connection to the Protein Data Bank. Ensure your agent has appropriate network access for optimal performance.
Tags
TrustedSkills Verification
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Security Audits
| Gen Agent Trust Hub | Pass |
| Socket | Pass |
| Snyk | Pass |
🌐 Community
Passed automated security scans.