# Alphafold Database

Access AlphaFold's 200M+ AI-predicted protein structures.

- Repository: https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills (3090 stars)
- Category: Engineering
- License: see repository
- Last updated: 2026-07-21
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill alphafold-database -g -a claude-code -y`
Codex: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill alphafold-database -g -a codex -y`
Cursor: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill alphafold-database -g -a cursor -y`
Gemini CLI: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill alphafold-database -g -a gemini-cli -y`

## Description

Access AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# AlphaFold Database

## Overview

AlphaFold DB is a public repository of AI-predicted 3D protein structures for over 200 million proteins, maintained by DeepMind and EMBL-EBI. Access structure predictions with confidence metrics, download coordinate files, retrieve bulk datasets, and integrate predictions into computational workflows.

## When to Use This Skill

This skill should be used when working with AI-predicted protein structures in scenarios such as:

- Retrieving protein structure predictions by UniProt ID or protein name
- Downloading PDB/mmCIF coordinate files for structural analysis
- Analyzing prediction confidence metrics (pLDDT, PAE) to assess reliability
- Accessing bulk proteome datasets via Google Cloud Platform
- Comparing predicted structures with experimental data
- Performing structure-based drug discovery or protein engineering
- Building structural models for proteins lacking experimental structures
- Integrating AlphaFold predictions into computational pipelines

## Core Capabilities

### 1. Searching and Retrieving Predictions

**Using Biopython (Recommended):**

The Biopython library provides the simplest interface for retrieving AlphaFold structures:

```python
from Bio.PDB import alphafold_db

# Get all predictions for a UniProt accession
predictions = list(alphafold_db.get_predictions("P00520"))

# Download structure file (mmCIF format)
for prediction in predictions:
    cif_file = alphafold_db.download_cif_for(prediction, directory="./structures")
    print(f"Downloaded: {cif_file}")

# Get Structure objects directly
from Bio.PDB import MMCIFParser
structures = list(alphafold_db.get_structural_models_for("P00520"))
```

**Direct API Access:**

Query predictions using REST endpoints:

```python
import requests

# Get prediction metadata for a UniProt accession
uniprot_id = "P00520"
api_url = f"https://alphafold.ebi.ac.uk/api/prediction/{uniprot_id}"
response = requests.get(api_url)
prediction_data = response.json()

The rest: https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/blob/HEAD/skills/alphafold-database/SKILL.md