Search protein folding research data from Clarity Protocol. Use when the user asks to search variants, query protein research, find fold results, or explore disease-specific protein data. Capabilities: list variants by disease or protein name, get API info.
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---
name: clarity-research
description: "Search protein folding research data from Clarity Protocol. Use when the user asks to search variants, query protein research, find fold results, or explore disease-specific protein data. Capabilities: list variants by disease or protein name, get API info."
---
# Clarity Research Skill
Search protein folding research data from Clarity Protocol, a community-driven platform for protein mutation analysis using AlphaFold2 via ColabFold.
## Quick Start
List all available variants:
```bash
python scripts/query_variants.py
```
Filter by disease:
```bash
python scripts/query_variants.py --disease Alzheimer
```
Filter by protein name:
```bash
python scripts/query_variants.py --protein-name MAPT
```
## Output Fields
Each variant result includes:
- `id`: Unique fold identifier
- `protein_name`: Protein name (e.g., "tau", "APP")
- `variant`: Mutation notation (e.g., "P301L", "A246E")
- `disease`: Associated disease
- `uniprot_id`: UniProt database identifier
- `average_confidence`: AlphaFold confidence score (0-100)
- `created_at`: When the fold was created
## Rate Limits
- **Anonymous (no API key)**: 10 requests/minute
- **With API key**: 100 requests/minute
To use an API key, set the `CLARITY_API_KEY` environment variable:
```bash
export CLARITY_API_KEY=your_key_here
python scripts/query_variants.py
```
Get your API key at https://clarityprotocol.io
## Error Handling
**404 Not Found**: The endpoint or resource does not exist.
**429 Rate Limit**: You've exceeded the rate limit. The script will display how long to wait before retrying.
**500 Server Error**: The API server encountered an error. Try again later.
**Timeout**: The request took longer than 30 seconds. The server may be under heavy load.
## Pagination
Results are paginated. The API returns a `next_cursor` field if more results are available. The script automatically handles pagination for typical queries.
## Use Cases
- Explore available protein variants for a specific disease
- Find all folded mutations for a particular protein
- Get an overview of research data available in Clarity Protocol
- Identify fold IDs for detailed analysis with other skills
