# RCSB PDB

Connects your agent to the Protein Data Bank to search macromolecular structures, inspect assembly details, and align sequences with UniProt.

- MCP server · `type=mcp` · Claude Code, Codex, Cursor, GitHub Copilot, Windsurf (Devin Desktop), Cline, Zed, Gemini CLI · ★ 11
- Author: rcsb
- License: MIT · policy=link-only · description only; the file stays with the author
- Source: https://github.com/rcsb/rcsb-mcp
- Updated: 2026-10-23
- HTML: https://affpapa.org/en/nevibecode/mcp/rcsb-pdb

## What it 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`.

## Requirements
- Needs: Python and uv (commands run via uvx)

## Install

### Claude Code (native platform)

**Platform CLI**
```bash
claude mcp add rcsb-mcp -- uvx rcsb-mcp
```
uvx runs the command named after the package; if the README names another one, use uvx --from rcsb-mcp <command>

### Codex

**Platform CLI**
```bash
codex mcp add rcsb-pdb -- uvx rcsb-mcp
```
uvx runs the command named after the package; if the README names another one, use uvx --from rcsb-mcp <command>

### Cursor

**Config file**
File `.cursor/mcp.json`:
```json
{
    "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>

### GitHub Copilot

**Config file**
File `.vscode/mcp.json`:
```json
{
    "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>

### Gemini CLI

**Platform CLI**
```bash
gemini mcp add rcsb-pdb uvx rcsb-mcp
```
uvx runs the command named after the package; if the README names another one, use uvx --from rcsb-mcp <command>

## When to use it
- 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
- 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

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