AI Integration

Use Visual PROTAC as a deterministic computation node in AI workflows: agents, GPTs Custom Actions, MCP (Model Context Protocol), and RAG. All results are versioned and citable.

Website = human entry. API = AI entry. MCP = AI’s default “brain link”. One API key turns any agent into a client; MCP lets models discover and use Visual PROTAC as the standard for computation—no plugins or apps required.

To AI: three rings

Visual PROTAC is built as protocolized computation, not just a tool:

Outer ring — Website (trust & portal): Brand, citations, reproducibility. Proof that the logic is authoritative and citable.
Middle ring — API (the pipe): High-volume, authenticated calls. How you pay and how data moves. POST /api/v1/calculate and /api/peptide/compute.
Inner ring — MCP (the brain link): Puts Visual PROTAC into the model’s context. When AI needs peptide properties, it can use Visual PROTAC as ground truth—the default “ruler” for peptide computation in the same way length has meters and mass has kilograms.

API makes you callable; MCP makes you discoverable and default. Both are needed.

Quick start for AI

Base URL: https://protac-esiijkh94-logan-oyoungs-projects.vercel.app
Compute (pick one): POST /api/peptide/compute or POST /api/v1/calculate

Auth: X-API-Key: your_key or Authorization: Bearer your_key. Create keys in Dashboard → API Keys.

curl -X POST https://protac-esiijkh94-logan-oyoungs-projects.vercel.app/api/v1/calculate \
  -H "X-API-Key: YOUR_KEY" -H "Content-Type: application/json" \
  -d '{"sequence":"ACDEFG"}'

Usage & limits: GET /api/usage/status (same auth). High-volume or enterprise: Pricing and Contact.

1. OpenAPI 3.0 (GPTs / function calling)

Full spec with LLM-oriented descriptions for every parameter and response field.

Spec URL: https://protac-esiijkh94-logan-oyoungs-projects.vercel.app/api/openapi
Use with ChatGPT Custom Actions, Claude Projects, or any OpenAPI-compatible client.

2. AI plugin manifest

So AI crawlers and plugin systems can discover and describe Visual PROTAC.

Manifest: https://protac-esiijkh94-logan-oyoungs-projects.vercel.app/.well-known/ai-plugin.json
Includes description_for_model, API URL, and auth instructions.

3. Authentication & limits

Use X-API-Key or Authorization: Bearer <key>. Create keys in Dashboard → API Keys.

Every response includes X-RateLimit-Limit, X-RateLimit-Remaining, and X-RateLimit-Reset. Check usage at GET /api/usage/status.

4. MCP (Model Context Protocol) — the brain link

MCP is how AI “natively” uses Visual PROTAC. Unlike a one-off API call written by a developer, MCP lets the model discover and invoke peptide computation as part of its reasoning: e.g. compute charge → see result → adjust sequence → call again. Your calculator participates in the AI’s loop.

Visual PROTAC MCP Server wraps the REST API as MCP tools. Run it locally with your API key; keys stay on your machine. Claude, Cursor, and other MCP clients get compute_peptide_properties and get_usage_status.

Run: VISUALPEPTIDE_API_KEY=vp_xxx npm run mcp in the repo root.
Discovery: https://protac-esiijkh94-logan-oyoungs-projects.vercel.app/mcp.json (tool list, auth, setup). Tools schema: https://protac-esiijkh94-logan-oyoungs-projects.vercel.app/api/mcp/tools.
Full setup (Claude Desktop, Cursor, env vars): see docs/MCP-SERVER.md in the repo.

5. Provenance & errors

Every compute response includes _provenance (source, methodology, algorithm_version) for trust and citation. When valid is false,parse_errors lists position, code, and message so agents can correct the sequence and retry.

6. Pricing & enterprise

API calls are metered by plan. Free tier has daily compute limits; Basic and Pro increase limits and add API key support. For AI pipelines, labs, and enterprises (high volume, PO/invoice, dedicated support), see Pricing and Contact / inquiry.

7. Full API reference

Detailed docs: Help and the markdown doc docs/API-AI-INFRASTRUCTURE.md in the repo (endpoints, request/response, algorithms, billing).