RCSB PDB — Claude Code MCP server: what it does, how to install
Connects your agent to the Protein Data Bank to search macromolecular structures, inspect assembly details, and align sequences with UniProt.
claude mcp add rcsb-mcp -- uvx rcsb-mcpWhat RCSB PDB does
The server bridges an LLM to three distinct RCSB services: the Search API, the Data GraphQL endpoint, and the Sequence Coordinates API. Structure searches follow a decoupled two-step model. Specialized builders assemble query JSON locally without making web calls, and only rcsb_search_request executes the search over the network to fetch matching identifiers.
You can combine multiple criteria using rcsb_query_composer. It links MMseqs2 sequence comparisons, chemical InChI descriptors, and taxonomy filters via boolean operators. Dedicated lookup tools resolve plain-text disease names or enzyme descriptions into standard MONDO, Gene Ontology, and EC identifiers.
The runtime expects uvx on your system path. Batch retrieval with all_hits=True fails on query results above 10,000 matches, meaning larger datasets require standard pagination with limit and offset.
What it helps with
- query Protein Data Bank entries by sequence similarity or 3D structural motif
- fetch macromolecular assemblies and ligand properties from the GraphQL Data API
- cross-reference residue positions across PDB, UniProt, and NCBI
- resolve biological terms into Gene Ontology or Enzyme Commission codes
Example prompts for the agent
- Search for Cas9 structures with resolution better than 2.5 angstroms using rcsb_query_attribute
- Find protein homologs by sequence similarity using rcsb_query_sequence
- Retrieve annotations and assembly details for entry 4HHB via the Data API
How to install RCSB PDB
Platform CLI
claude mcp add rcsb-mcp -- uvx rcsb-mcpuvx runs the command named after the package; if the README names another one, use uvx --from rcsb-mcp <command>
Platform CLI
codex mcp add rcsb-pdb -- uvx rcsb-mcpuvx runs the command named after the package; if the README names another one, use uvx --from rcsb-mcp <command>
Config file
{
"mcpServers": {
"rcsb-pdb": {
"command": "uvx",
"args": [
"rcsb-mcp"
]
}
}
}uvx runs the command named after the package; if the README names another one, use uvx --from rcsb-mcp <command>
Config file
{
"servers": {
"rcsb-pdb": {
"type": "stdio",
"command": "uvx",
"args": [
"rcsb-mcp"
]
}
}
}uvx runs the command named after the package; if the README names another one, use uvx --from rcsb-mcp <command>
Platform CLI
gemini mcp add rcsb-pdb uvx rcsb-mcpuvx runs the command named after the package; if the README names another one, use uvx --from rcsb-mcp <command>
Step by step, with commands for each platform: How to add an MCP server to Claude Code, Codex, Cursor, VS Code, Gemini CLI and more
Questions about RCSB PDB
How to install RCSB PDB in Claude Code?
Run claude mcp add rcsb-pdb -- uvx rcsb-mcp in your terminal. You must have uvx installed in your environment.
What does the RCSB PDB MCP server do?
It gives an LLM programmatic access to Protein Data Bank APIs to construct multi-criteria structure queries, fetch GraphQL metadata, and map coordinates.
Why does searching require two separate steps?
Query-builder tools only generate structured JSON objects offline. Network requests happen strictly when passing that document into rcsb_search_request.
