Clarity Research

Search protein folding research data from Clarity Protocol. Use when the user asks to search variants, query protein research, find fold results, or explore...

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:

python scripts/query_variants.py

Filter by disease:

python scripts/query_variants.py --disease Alzheimer

Filter by protein name:

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:

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