How do I install the Clarity Research skill?

Run npx skillmds@latest add modbender/clarity-research in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Clarity Research safe to use?

This skill has not completed SkillMD's automated safety review yet. Independent scanners report: SkillSpector: PASS, Skill Scanner: PASS. Capability flags: executes scripts, makes network calls. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Clarity Research?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Clarity Research free to use?

Yes. Installing skills from SkillMD is free. This skill is licensed under MIT.

Who published Clarity Research?

modbender (@modbender) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Clarity Research by modbender — Agent Skill

Name: Clarity Research
Rating: 4.5 (4 reviews)
Author: modbender

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 disease-specific protein data. Capabilities: list variants by disease or protein name, get API info.

modbender Updated Sep 9, 2026 12 repo stars

File contents

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

---name: clarity-researchdescription: 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--- # 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

Frequently asked questions