# AlphaFold

> Use this tool when you need to predict and analyze protein structures, solve problems in structural biology research, and streamline bioinformatics applications. AlphaFold provides comprehensive access to protein structure data through 22 specialized tools, accepting inputs like UniProt ID or organism and outputting structures in multiple formats. It is ideal for use cases requiring programmatic access to high-quality protein structure predictions, confidence analysis, and comparative analysis.

Canonical page: https://skillsregistry.net/skills/augmented-nature-alphafold  
JSON: https://api.skillsregistry.net/v1/skills/augmented-nature-alphafold

## Description

The AlphaFold MCP Server provides comprehensive access to DeepMind's AlphaFold Protein Structure Database through 22 specialized tools covering structure retrieval, confidence analysis, batch processing, and comparative analysis. Built by Augmented Nature, it integrates directly with the AlphaFold API to enable protein structure searches by UniProt ID or organism, download structures in multiple formats (PDB, CIF, mmCIF), analyze per-residue confidence scores, and export data for visualization tools like PyMOL and ChimeraX. The server is particularly valuable for structural biology research, protein analysis workflows, and bioinformatics applications where users need programmatic access to high-quality protein structure predictions without manually navigating the AlphaFold database interface.

## Trust

- **Trust score (0–1):** 0.97
- **Verification tier:** verified
- **Last scanned:** 2026-09-28

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** database
- **Updated:** 2026-09-28

## Source

- **Source listing:** [PulseMCP](https://www.pulsemcp.com/servers/augmented-nature-alphafold)
- **Repository:** <https://github.com/augmented-nature/alphafold-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-alphafold"
    }
  }
}
```

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