Pdb Database
Helps with AI, database as part of working with databases and data persistence workflows.
Install on your platform
We auto-selected Claude Code based on this skill’s supported platforms.
Run in terminal (recommended)
claude mcp add k-dense-ai-pdb-database npx -- -y @trustedskills/k-dense-ai-pdb-database
Or manually add to ~/.claude/settings.json
{
"mcpServers": {
"k-dense-ai-pdb-database": {
"command": "npx",
"args": [
"-y",
"@trustedskills/k-dense-ai-pdb-database"
]
}
}
}Requires Claude Code (claude CLI). Run claude --version to verify your install.
About This Skill
What it does
This skill allows AI agents to query and retrieve information from the Protein Data Bank (PDB), a repository of 3D structural data of large biological molecules. It can extract details like protein names, experimental conditions, resolution, and sequence lengths. The agent can also provide links to the full PDB entry for further investigation.
When to use it
- Researching protein structures for drug discovery or understanding disease mechanisms.
- Generating reports on specific proteins based on their PDB entries.
- Automating data extraction from PDB records for analysis pipelines.
- Providing users with information about the experimental methods used to determine a protein's structure.
Key capabilities
- PDB entry retrieval by ID or name
- Extraction of structural details (resolution, sequence length)
- Retrieval of experimental conditions
- Link provision to full PDB entry
Example prompts
- "Get me the PDB information for 1AKE."
- "What is the resolution of the structure in PDB ID 4HHB?"
- "Find all entries with 'lysozyme' in their name and tell me their resolutions."
Tips & gotchas
The skill relies on accurate PDB identifiers. Ensure you provide valid PDB IDs or names for optimal results.
Tags
TrustedSkills Verification
Unlike other registries that point to live repositories, TrustedSkills pins every skill to a verified commit hash. This protects you from malicious updates — what you install today is exactly what was reviewed and verified.
Security Audits
| Gen Agent Trust Hub | Pass |
| Socket | Pass |
| Snyk | Pass |
🌐 Community
Passed automated security scans.