How do I install the Clarity Submit skill?

Run npx skillmds@latest add modbender/clarity-submit 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 Submit 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. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Clarity Submit?

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 Submit free to use?

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

Who published Clarity Submit?

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

Clarity Submit by modbender — Agent Skill

Name: Clarity Submit
Rating: 4.2 (5 reviews)
Author: modbender

Clarity Submit

Submit a protein variant hypothesis to Clarity Protocol for validation and folding. Use when the user asks to submit a hypothesis, propose a protein variant, queue a fold, or investigate a mutation. Requires CLARITY_WRITE_KEY env var. Capabilities: submit hypothesis, check submission status.

modbender Updated Sep 9, 2026 12 repo stars

File contents

Clarity Submit Skill

Submit protein variant hypotheses to Clarity Protocol for automated validation and ColabFold structural prediction.

Quick Start

Submit a hypothesis:

python scripts/submit_hypothesis.py --protein SOD1 --variant A4V --rationale "ALS-linked mutation with unknown structural impact"

Submit with optional fields:

python scripts/submit_hypothesis.py --protein MAPT --variant P301L --rationale "Tau pathology in frontotemporal dementia" --wallet "YOUR_SOLANA_WALLET"

Check hypothesis status:

python scripts/check_status.py --id 42

Setup

Set your write API key:

export CLARITY_WRITE_KEY=your_write_key_here

Contact the Clarity Protocol team to request a write API key.

What Happens After Submission

Feasibility validation runs automatically against UniProt, ClinVar, gnomAD, and PubMed
If validated, the hypothesis is auto-queued for ColabFold structural prediction
Four AI research agents continuously monitor the variant for new findings
Results are available at the tracking URL returned after submission

Request Fields

--protein (required): Protein name (e.g., SOD1, MAPT, APP, SNCA)
--variant (required): Variant notation (e.g., A4V, P301L, G2019S)
--rationale (required): Why this variant is worth investigating (min 10 characters)
--disease (optional): Disease area (auto-detected from protein if omitted)
--wallet (optional): Solana wallet address for $FOLD reward eligibility

Response Fields

id: Unique hypothesis identifier
protein_name: Normalized protein name
variant_notation: Variant as submitted
status: Current status (submitted, validating, validated, queued, folding, complete, rejected)
tracking_url: URL to track progress on clarityprotocol.io

Rate Limits

Write (POST): 10 submissions per day per key
Read (GET): 100 requests per minute per key

Size Limits

Proteins up to 1,500 residues can be folded. Larger proteins (e.g., LRRK2 at 2,527 residues) exceed hardware capacity and will be rejected during validation.

Error Handling

403 Forbidden: Invalid or missing write API key. Set CLARITY_WRITE_KEY env var.

422 Validation Error: Invalid input (protein name empty, rationale too short, etc.).

429 Rate Limit: You've exceeded 10 submissions/day. Wait until tomorrow.

Use Cases

Programmatically submit variants for investigation
Integrate Clarity Protocol into research pipelines
Batch submission of variants of interest
Agent-driven hypothesis generation and submission

---name: clarity-submitdescription: Submit a protein variant hypothesis to Clarity Protocol for validation and folding. Use when the user asks to submit a hypothesis, propose a protein variant, queue a fold, or investigate a mutation. Requires CLARITY_WRITE_KEY env var. Capabilities: submit hypothesis, check submission status.license: MIT--- # Clarity Submit Skill Submit protein variant hypotheses to Clarity Protocol for automated validation and ColabFold structural prediction. ## Quick Start Submit a hypothesis: ```bash python scripts/submit_hypothesis.py --protein SOD1 --variant A4V --rationale "ALS-linked mutation with unknown structural impact" ``` Submit with optional fields: ```bash python scripts/submit_hypothesis.py --protein MAPT --variant P301L --rationale "Tau pathology in frontotemporal dementia" --wallet "YOUR_SOLANA_WALLET" ``` Check hypothesis status: ```bash python scripts/check_status.py --id 42 ``` ## Setup Set your write API key: ```bash export CLARITY_WRITE_KEY=your_write_key_here ``` Contact the Clarity Protocol team to request a write API key. ## What Happens After Submission 1. **Feasibility validation** runs automatically against UniProt, ClinVar, gnomAD, and PubMed 2. If validated, the hypothesis is **auto-queued** for ColabFold structural prediction 3. Four AI research agents continuously monitor the variant for new findings 4. Results are available at the tracking URL returned after submission ## Request Fields - `--protein` (required): Protein name (e.g., SOD1, MAPT, APP, SNCA) - `--variant` (required): Variant notation (e.g., A4V, P301L, G2019S) - `--rationale` (required): Why this variant is worth investigating (min 10 characters) - `--disease` (optional): Disease area (auto-detected from protein if omitted) - `--wallet` (optional): Solana wallet address for $FOLD reward eligibility ## Response Fields - `id`: Unique hypothesis identifier - `protein_name`: Normalized protein name - `variant_notation`: Variant as submitted - `status`: Current status (submitted, validating, validated, queued, folding, complete, rejected) - `tracking_url`: URL to track progress on clarityprotocol.io ## Rate Limits - **Write (POST)**: 10 submissions per day per key - **Read (GET)**: 100 requests per minute per key ## Size Limits Proteins up to 1,500 residues can be folded. Larger proteins (e.g., LRRK2 at 2,527 residues) exceed hardware capacity and will be rejected during validation. ## Error Handling **403 Forbidden**: Invalid or missing write API key. Set CLARITY_WRITE_KEY env var. **422 Validation Error**: Invalid input (protein name empty, rationale too short, etc.). **429 Rate Limit**: You've exceeded 10 submissions/day. Wait until tomorrow. ## Use Cases - Programmatically submit variants for investigation - Integrate Clarity Protocol into research pipelines - Batch submission of variants of interest - Agent-driven hypothesis generation and submission

Frequently asked questions