PDB MCP Server
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Instructions
Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.
This server publishes no instructions, or was last inspected before Glama recorded them.
Capabilities
Server capabilities have not been inspected yet.
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| search_structuresC | Search PDB database for protein structures by keyword, protein name, or PDB ID |
| get_structure_infoC | Get detailed information for a specific PDB structure |
| download_structureC | Download structure coordinates in various formats |
| search_by_uniprotC | Find PDB structures associated with a UniProt accession |
| get_structure_qualityC | Get structure quality metrics and validation data |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
TDQS
Scored across 5 tools
Each tool has a clearly distinct purpose: downloading structure data, retrieving structure metadata, accessing quality metrics, searching by UniProt ID, and general keyword/ID search. There is no overlap in functionality, making tool selection straightforward for an agent.
All tool names follow a consistent verb_noun pattern with snake_case (e.g., download_structure, get_structure_info, search_by_uniprot). The naming is uniform and predictable across all five tools.
Five tools is well-scoped for a PDB (Protein Data Bank) server, covering core operations like data retrieval, search, and quality assessment without being too sparse or overwhelming. Each tool serves a clear, necessary function.
The toolset provides strong coverage for querying and retrieving PDB structure data, including search, info, quality, and download functions. A minor gap might be the lack of tools for advanced filtering or batch operations, but core workflows are well-supported.