# PDB MCP Server

> PDB MCP Server — augmented-nature-pdb-mcp-server. Use this tool when you need to manage and process Protein Data Bank (PDB) files, solve structural biology problems, and analyze molecular structures. It provides a server-based interface for inputting PDB files and outputting processed data, enabling efficient management of molecular coordinates and related information. Ideal for use in bioinformatics, structural biology, and related research contexts.

Canonical page: https://skillsregistry.net/skills/augmented-nature-pdb-mcp-server  
JSON: https://api.skillsregistry.net/v1/skills/augmented-nature-pdb-mcp-server

## Description

A Model Context Protocol (MCP) server that provides access to the Protein Data Bank (PDB) - the worldwide repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.

## Trust

- **Trust score (0–1):** 0.99
- **Verification tier:** verified
- **Last scanned:** 2026-09-19

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** other
- **Updated:** 2026-09-19

## Source

- **Source listing:** [Glama](https://glama.ai/mcp/servers/l6se31dqou)
- **Repository:** <https://github.com/Augmented-Nature/PDB-MCP-Server>

## Use it

Resolve this record through the SkillsRegistry MCP server (no auth, read-only):

```
claude mcp add --transport http --scope user skillsregistry https://api.skillsregistry.net/mcp
```

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "get_skill",
    "arguments": {
      "slug": "augmented-nature-pdb-mcp-server"
    }
  }
}
```

REST: `GET https://api.skillsregistry.net/v1/skills/augmented-nature-pdb-mcp-server` · pull for local use: `GET https://api.skillsregistry.net/v1/skills/augmented-nature-pdb-mcp-server/pull`

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SkillsRegistry indexes agent skills from public registries and GitHub. Skills we have analysed are scanned with Circle-IR and scored on six dimensions; each listing states its scan coverage. More: https://skillsregistry.net/llms.txt