Protein Data Bank
This MCP server provides AI assistants with access to the Protein Data Bank (PDB) for structural biology research, built by Augmented Nature using TypeScript and the Model Context Protocol SDK. The implementation offers comprehensive tools for searching protein structures by keyword or UniProt ID, retrieving detailed structure information and coordinates in multiple formats (PDB, mmCIF, XML), downloading structure files with biological assembly support, and accessing structure quality metrics including validation data and refinement statistics. Built with dual API integration using both RCSB PDB's REST API and search services, it supports advanced filtering by experimental method and resolution range, making it valuable for structural biologists analyzing protein structures, researchers conducting comparative structural studies, and AI applications requiring programmatic access to crystallographic data and molecular structure information.
Composite of vulnerability cleanliness, spec conformance, provenance, stability, and usage signals — scanned and weighted by Cognium. Human and agent signals are tracked separately.
View full trust & usage report →Metadata
- Version
- 1.0.0
- Skill type
- atomic
- Execution layer
- mcp-remote
- Category
- monitoring
- Source
- PulseMCP
- Repository
- github.com/augmented-nature/pdb-mcp-server
- Author type
- human
- Updated
- 2026-04-25
Use via MCP
Resolve Protein Data Bank from your agent
Streamable HTTP transport at https://api.skillsregistry.net/mcp. No auth for read tools. Discovery: .well-known/mcp.json.
One command in your shell — Claude Code wires it up and verifies the connection. Run /mcp in any session to confirm.
claude mcp add --transport http --scope user skillsregistry https://api.skillsregistry.net/mcp--scope user for --scope project to commit it to .mcp.json.