---
title: Connect AI agents with MCP
url: https://www.moldraw.com/docs/developers/connect-ai-agents-to-moldraw-with-mcp/
section: Embed and developer tools
updated: 2026-10-20
publisher: LabCanvas
---

# Connect AI agents with MCP

> Add https://mcp.moldraw.com/mcp as a remote MCP server in your AI app. Sign in with your MolDraw account and click Approve. The agent can then search compounds, create and edit structures, export files and save designs to My designs.

MCP (Model Context Protocol) is a standard way for AI apps to use outside tools. MolDraw runs a hosted MCP server. An AI agent can use it to draw and edit structures with the same operations as the editor. This is separate from the [AI chat inside MolDraw](https://www.moldraw.com/docs/ai/how-to-set-up-ai-providers-and-api-keys/), which uses your own API key.

## Connect your AI app

1. Open the connector or MCP settings of your AI app.
2. Add a remote server with the URL `https://mcp.moldraw.com/mcp`.
3. Your browser opens MolDraw. Sign in, or create a free account.
4. Read the page **Let ... use MolDraw**. It lists who is asking and what the app can do.
5. If asked, add your name and designation. Then click **Approve**.
6. Back in your AI app, ask it to draw a structure.

The same address works for every MCP client. You sign in on the MolDraw page, so your MolDraw password is never shared with the AI app. You can disconnect later from the app that asked for access.

## What the agent can do

| Tool | What it does |
| --- | --- |
| Search molecule | Finds a compound by name, CAS number or PubChem CID |
| Create structure | Starts a working structure from SMILES, a molfile or a name |
| Get molecule | Reads counts, SMILES, formula and atom ids, with an image preview |
| Modify structure | Adds groups, changes atoms or bonds, deletes atoms, adds fragments, swaps substructures |
| Convert structure | Converts between SMILES, molfile and 3D SDF |
| Export structure | Exports SVG, PNG, molfile, SMILES or 3D SDF |
| Save, list and open designs | Reads and writes your [My designs](https://www.moldraw.com/docs/account/how-to-manage-my-designs-and-document-tabs/) |
| List editor tools and Editor action | Runs named editor operations: reaction schemes with plus signs and reagent arrows, text labels, alignment, library templates, glassware, orbitals, rings, colours, clean up and aromatize |

Results include an image of the structure and an **open in MolDraw** link. Apps that support MCP Apps also show an inline MolDraw editor in the chat.

## Example prompts

- *Draw caffeine.*
- *Change the methyl group at position 7 to ethyl.*
- *Give me the SMILES, then export SVG.*
- *Draw the Claisen condensation as a scheme with reagents on the arrow.*

## Privacy and limits

- Structures the agent creates are working documents. They last 7 days unless you save them as a design.
- Saved designs go to your normal My designs library.
- Chat transcripts are not stored. The server only sees tool calls and structure data.
- Every working document is tied to your account.
- Each account can make up to 120 tool calls per minute.
- Tools that change a structure are marked apart from tools that only read.

Read the full [MCP privacy and security notes](https://www.moldraw.com/pages/mcp-privacy.html).

## Common problems

| Symptom | Fix |
| --- | --- |
| The app cannot connect | Check the URL ends in `/mcp`. Your app must support remote MCP servers over HTTP. |
| The sign in page says the link is missing data | Start the connection again from your AI app. Do not open the consent page by hand. |
| The agent's link opens an old structure | Working documents expire after 7 days. Ask the agent to save a design. |
| Calls fail after many quick edits | You hit the rate limit. Wait a minute. |

For links the agent returns, see [URL parameters and deep links](https://www.moldraw.com/docs/developers/moldraw-url-parameters-and-deep-links/). For text based mechanisms an agent can write, see [MolScript](https://www.moldraw.com/docs/developers/molscript-language-for-reactions-and-mechanisms/).

## Questions and answers

**Does MolDraw have an MCP server?**
Yes. Point any MCP client at https://mcp.moldraw.com/mcp and sign in with your MolDraw account.

**Do I need a MolDraw account to use the MCP connector?**
Yes. The connector signs in with your MolDraw account. A free account works.

**Can the AI agent save drawings to My designs?**
Yes. It can save, list and open your designs. Other working structures expire after 7 days.

**Does the MCP connector need my AI API key?**
No. Your AI app runs the model. MolDraw only provides the drawing tools.

## Related pages

- [AI assistant](https://www.moldraw.com/docs/ai/how-to-use-the-ai-chemistry-assistant/)
- [AI providers and API keys](https://www.moldraw.com/docs/ai/how-to-set-up-ai-providers-and-api-keys/)
- [URL parameters and deep links](https://www.moldraw.com/docs/developers/moldraw-url-parameters-and-deep-links/)
- [MolScript](https://www.moldraw.com/docs/developers/molscript-language-for-reactions-and-mechanisms/)