clarity-research

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.
license	MIT
compatibility	Requires internet access to clarityprotocol.io. Optional CLARITY_API_KEY env var for 100 req/min (vs 10 req/min).
metadata	{"author":"clarity-protocol","version":"1.0.0","homepage":"https://clarityprotocol.io"}

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