# Rcsb Pdb (npm · @pipeworx/mcp-rcsb-pdb)

RCSB PDB MCP — experimentally determined macromolecular structures.

- Trust score: 78/100 (medium)
- Registry status: active
- Liveness: live
- Owner verified: no
- Last scored: 2026-11-05

## Components

- remote · `gateway.pipeworx.io`: 77/100, [markdown](https://verifymcp.io/servers/pipeworx-io-rcsb-pdb/rcsb-pdb-mcp.md), [page](https://verifymcp.io/servers/pipeworx-io-rcsb-pdb/rcsb-pdb-mcp)
- npm · `@pipeworx/mcp-rcsb-pdb`: 78/100 (this document), [markdown](https://verifymcp.io/servers/pipeworx-io-rcsb-pdb/pipeworx-mcp-rcsb-pdb.md), [page](https://verifymcp.io/servers/pipeworx-io-rcsb-pdb/pipeworx-mcp-rcsb-pdb)

## Channel facts

- Registry: `npm`
- Package: `@pipeworx/mcp-rcsb-pdb`
- Version: `0.2.1`
- Transport: `stdio`

## Trust breakdown

How this component scores in each security and reliability category. Every signal is checked automatically from public evidence about the published package, including repeated runs of it in an isolated sandbox, and we only credit what we can confirm. Scores are 0–100 per category. Scoring method: https://verifymcp.io/docs/scoring (what has changed: https://verifymcp.io/docs/scoring/changelog)

Scored 2026-11-05.

- **Supply Chain Security**: 100/100
  - No malware found by supply-chain analysis.
  - No known CVEs affecting this package version or its production dependencies.
  - No install/post-install scripts declared.
  - No production dependencies, so there is no dependency health to assess.
- **Provenance & Transparency**: 97/100
  - Source repository is publicly reachable at the declared URL.
  - Cryptographically verified build provenance (signed, bound to pipeworx-io/mcp-rcsb-pdb).
  - Clear OSI-approved license (MIT).
  - Actively maintained (last published 0 days ago).
  - Disclosure check failed: no security disclosure policy was found in the source repository.
- **Schema Quality & AI Usability**: 69/100
  - AI-judged instruction clarity (good).
  - Tool/resource definitions use about 683 tokens (~113/item across 6 items; 6 tools + 0 resources), lean.
  - Usage-examples check failed: none of the tools include examples.
- **Stability & Change Management**: 3/100
  - Stability observed for 1 of 30 days with no destabilising changes; credit accrues until the full window elapses.
- **Tool Coverage**: 76/100
  - 100% of tools have a non-trivial description (not blank, and not just the tool's name).
  - 27% of tool parameters carry a description.
- **Tool Safety**: 100/100
  - No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.
  - We read all 6 captured tool definition(s), and no name or description among them implies an irreversible operation.
  - An AI judge read all 7 captured unit(s) of tool text and found none that tries to manipulate the model reading it.
- **Capabilities**: 100/100
  - Implements a supported MCP spec version (2025-11-25); the latest is 2026-07-28.

## Install

### How do I install the Rcsb Pdb MCP server?

Rcsb Pdb runs locally as an npm package, launched with npx -y @pipeworx/mcp-rcsb-pdb. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.

### Claude

```bash
claude mcp add pipeworx-io-rcsb-pdb -- npx -y @pipeworx/mcp-rcsb-pdb
```

### Cursor

```json
{
  "mcpServers": {
    "pipeworx-io-rcsb-pdb": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-rcsb-pdb"
      ]
    }
  }
}
```

### VS Code

```json
{
  "servers": {
    "pipeworx-io-rcsb-pdb": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-rcsb-pdb"
      ]
    }
  }
}
```

### Codex

```bash
codex mcp add pipeworx-io-rcsb-pdb -- npx -y @pipeworx/mcp-rcsb-pdb
```

### opencode

```json
{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "pipeworx-io-rcsb-pdb": {
      "type": "local",
      "command": [
        "npx",
        "-y",
        "@pipeworx/mcp-rcsb-pdb"
      ],
      "enabled": true
    }
  }
}
```

### OpenClaw

```bash
openclaw mcp add pipeworx-io-rcsb-pdb --command npx --arg -y --arg @pipeworx/mcp-rcsb-pdb
```

### Hermes

```yaml
mcp_servers:
  pipeworx-io-rcsb-pdb:
    command: "npx"
    args: ["-y", "@pipeworx/mcp-rcsb-pdb"]
```

### Netclaw

```json
{
  "McpServers": {
    "pipeworx-io-rcsb-pdb": {
      "Transport": "stdio",
      "Command": "npx",
      "Arguments": [
        "-y",
        "@pipeworx/mcp-rcsb-pdb"
      ]
    }
  }
}
```

### Vellum

```bash
assistant mcp add pipeworx-io-rcsb-pdb -t stdio -c npx -a -y @pipeworx/mcp-rcsb-pdb
```

### Other

```json
{
  "mcpServers": {
    "pipeworx-io-rcsb-pdb": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-rcsb-pdb"
      ]
    }
  }
}
```

## Changelog

Every change recorded for this component, newest first. Days that predate change tracking, or that we cannot explain, say so: "we were watching and nothing happened" and "we were not watching" are different claims.

### 2026-11-04 (score 78)

First indexed and scored.

## MCP tools (6)

### `search` (~166 tokens)

"Find protein structure of [target]" / "search PDB for [protein]" / "is there a crystal structure of [X]" / "[disease target] structures" / "CRISPR / kinase / GPCR structures" — text search the RCSB PDB (the global archive of experimentally-determined 3D protein/RNA/DNA structures). Returns matching PDB IDs you can pass to `structure` or `summary`. Use for structural biology, drug design, protein characterization.

Input parameters:

- `limit` (number): 1-1000 (default 25).
- `query` (string, required): Free-text, e.g. "CRISPR Cas9".
- `return_type` (string): entry (default) | polymer_entity | non_polymer_entity | assembly

### `structure` (~106 tokens)

"PDB entry [1abc] details" / "fetch protein structure [pdb_id]" / "metadata for [PDB ID]" — full PDB entry record by ID (e.g. "1abc", "7BV2"). Returns experimental method (X-ray / cryo-EM / NMR), resolution, authors, deposition date, organism, ligands, related entities. Use after `search` to inspect a specific structure.

Input parameters:

- `pdb_id` (string, required)

### `polymer_entity` (~95 tokens)

"Chain [N] of PDB [ID]" / "sequence of chain in [pdb_id]" — fetch the polymer-entity (protein/DNA/RNA chain) metadata for a specific PDB entry. Returns sequence, source organism, UniProt cross-references, GO annotations. Use to drill into one chain of a multi-chain structure.

Input parameters:

- `entity_id` (string, required)
- `pdb_id` (string, required)

### `ligand` (~95 tokens)

"Ligand / cofactor / drug bound to [pdb_id]" / "small molecule in [PDB entry]" — fetch a non-polymer ligand record (small molecule, cofactor, ion, or bound drug) for a PDB entry. Use to inspect what's bound in a co-crystal structure — common in drug discovery / SBDD.

Input parameters:

- `ligand_id` (string, required)
- `pdb_id` (string, required)

### `assembly` (~94 tokens)

"Biological assembly of [pdb_id]" / "functional oligomer for [PDB entry]" — fetch a biological assembly record (the functional oligomeric unit, which often differs from the crystallographic asymmetric unit). Use when you need the actual functional form of a protein (dimer / tetramer / etc.) rather than the crystal contents.

Input parameters:

- `assembly_id` (string)
- `pdb_id` (string, required)

### `summary` (~69 tokens)

Lightweight lookup for a PDB entry by 4-char ID: tries the RCSB UniProt endpoint first, falls back to the core entry record. Returns title, experimental method, resolution, and deposition date without the full polymer/ligand detail of `structure`.

Input parameters:

- `pdb_id` (string, required)

## Diagnostics

Captured diagnostic sections: Provenance, Dependencies. The full working is on the page: https://verifymcp.io/servers/pipeworx-io-rcsb-pdb/pipeworx-mcp-rcsb-pdb#diagnostics

## Score history

- 2026-11-05: 78
- 2026-11-04: 78

## Common questions

### What is the Rcsb Pdb MCP server?

Rcsb Pdb is an MCP server listed in the public MCP registry as io.github.pipeworx-io/rcsb-pdb. RCSB PDB MCP, experimentally determined macromolecular structures. This page covers its npm package (@pipeworx/mcp-rcsb-pdb).

### Is the Rcsb Pdb MCP server safe to use?

Rcsb Pdb scores 78 out of 100 on VerifyMCP. We found no known CVEs affecting it as of 5 November 2026. It declares no install or post-install scripts. Its build provenance is signed and verified. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.

### What tools does the Rcsb Pdb MCP server expose?

Rcsb Pdb exposes 6 tools: search, structure, polymer_entity, ligand, assembly, summary. Their descriptions and schemas cost roughly 625 tokens of context every time the server is loaded.

### Is the Rcsb Pdb MCP server still maintained?

Rcsb Pdb is still listed as active in the MCP registry. We last reached this channel on 5 November 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.

### What licence is the Rcsb Pdb MCP server under?

Rcsb Pdb declares the MIT licence, which is OSI-approved. That covers the source only, and says nothing about the cost of any service it calls.

## Links

- npm package: https://www.npmjs.com/package/@pipeworx/mcp-rcsb-pdb
- Socket report: https://socket.dev/npm/package/@pipeworx/mcp-rcsb-pdb
- Repository: https://github.com/pipeworx-io/mcp-rcsb-pdb
- Website: https://pipeworx.io/packs/rcsb-pdb
- Changelog RSS feed: https://verifymcp.io/servers/pipeworx-io-rcsb-pdb/pipeworx-mcp-rcsb-pdb.xml
- Changelog JSON feed: https://verifymcp.io/servers/pipeworx-io-rcsb-pdb/pipeworx-mcp-rcsb-pdb.json
- HTML version of this page: https://verifymcp.io/servers/pipeworx-io-rcsb-pdb/pipeworx-mcp-rcsb-pdb