An astronaut overseeing a futuristic data hub
Download PDFMarkdown Version

Connect PubChem to ChatGPT, Claude and Gemini

Set it up once and it works in ChatGPT, Claude, Cursor, and any other client you love. It all runs safely in the background, so you can relax and focus on what really matters. Pull molecular properties and structures directly into your AI agent.

Ask AI about this Connector

Developed, maintained, and hosted by Vinkius.

MCP VERIFIED · PRODUCTION READY · VINKIUS GUARANTEED

Waiting for input…

Works with modern AI clients that support MCP, including ChatGPT, Claude, Cursor, and more.

ChatGPTClaudeCursorPerplexityGeminiMicrosoft CopilotRaycastMeta AI

Your AI does the work. We keep it safe and sound.

No other AI tool gives you this. Your workflow runs in the client you already love, your account stays protected, and you decide what the agent can and cannot do. It is the whole reason to make the switch.

Each Connector lives inside our infrastructure, the same place where your workflow runs. The three things below are already part of it, working quietly in the background so you never have to think about them. Nothing to add, nothing to set up, nothing to worry about.

A futuristic MCP client docking bay
V8 Isolate01

Each Connector runs inside its own sealed environment.

Each Connector runs inside its own sealed V8 runtime — no access to your files, your system, or other servers. A Connector never sees past its own request.

Kill Switch02

One switch stops every agent. Instantly.

One action deactivates every Connector, revokes every token, and ends every session at once. AI Governance keeps the record.

FinOps per User03

Spending limits that pause instead of surprise.

Every user keeps their own connections and credentials, isolated from everyone else. Anything that would cross your spending limit is held for your approval, not billed.

Three controls, built into the layer your AI connects through.

Curated set · 3 capabilities

We ship only the actions that matter.

Capability set01 / 01

01-03

3 capabilities in this set.

Part of 3 available through PubChem.

  1. 01

    Get pubchem compound

    Retrieves the complete set of chemical data for a specific compound using its PubChem Compound ID (CID).

  2. 02

    Search pubchem

    Searches the database for compounds using names like aspirin or glucose to return molecular weight, SMILES, and other properties.

  3. 03

    Search pubchem formula

    Identifies all compounds that match a specific molecular formula provided by your agent.

Real work

What teams actually run

01

Lead Compound Screening

A chemist asks the agent to check the XLogP and hydrogen bond counts for a series of potential drug candidates.

02

Formula-Based Discovery

A researcher provides a molecular formula to find all existing compounds that match that specific structure.

03

Structure Verification

An agent verifies the SMILES or InChI notation for a specific CID to ensure data accuracy in a report.

04

Educational Research

A student uses the agent to quickly pull physicochemical data for coursework assignments.

Automate a task

Put PubChem to work on one thing.

Step-by-step automations your AI runs through this Connector: the workflow, the prompts to start with, and the exact capabilities behind each move.

One connector, every AI

PubChem works with the most popular AI clients.

These are the most popular clients, each with a step-by-step guide: one link, set up once, with governance and visibility built in. And because everything runs on the MCP standard, the same connection also works in any other compatible client — nothing to rebuild.

ClaudeClaudeChatGPTChatGPTGeminiGeminiPerplexityPerplexityGrokGrokMicrosoft CopilotMicrosoft CopilotCursorCursorVS CodeVS CodeWindsurfWindsurfJetBrainsJetBrainsClineClineLangChainLangChainVercel AI SDKVercel AI SDKLovableLovableZ.aiZ.aiRaycastRaycastQwen CodeQwen CodeKimi CodeKimi CodeLe ChatLe Chat

Building your own app? The connector is yours to use.

You don't need a client to put PubChem to work: the same hosted connection plugs into your own applications and agent code, with the same governance on every request. Build with it, chat with it — one connection for both.

Observed, not estimated

892ms average. Fast in production.

PubChem is checked daily against the live service.

Daily averagePeak 1138ms
Oct 3Today
Fastest day
719ms
Slowest day
1138ms
14-day trend
Slowing+13%

Connect your client

One URL. Every client.

Activate the Connector, copy your link, and paste it into the client you already use. 3 capabilities arrive ready to run.

Preview access · not provider authentication

The vk_preview_* token belongs to Vinkius preview infrastructure. It lets Claude discover and display the capabilities of PubChem, so you can see the experience inside your AI.

It does not authenticate your account with PubChem. Actions requiring credentials or live account data may not run until you activate the Connector and authorize the service.

PubChem Connector

You're all set. Choose your MCP client and follow the setup instructions.

Connector linkhttps://edge.vinkius.com/vk_preview_bfnYDABzlJ07TJu7Do9K5lCyve4Fg9F5YGb6KetY/mcp

Claude Desktop

Follow the steps below to connect in seconds.

  1. 1In Claude Desktop, open Settings → Connectors.
  2. 2Click “Add custom connector” and paste the connector link above as the remote MCP server URL.
  3. 3Click Add and start a new chat — PubChem capabilities are ready to use.
Configuration · claude_desktop_config.jsonCopy
{
  "mcpServers": {
    "pubchem-mcp": {
      "url": "https://edge.vinkius.com/vk_preview_bfnYDABzlJ07TJu7Do9K5lCyve4Fg9F5YGb6KetY/mcp"
    }
  }
}
  • Claude
  • ChatGPT
  • Cursor
  • VS Code
  • Windsurf
  • Claude Code
  • JetBrains
  • Cline

Step-by-step instructions for each client are in the guide. How to connect

Guided setup for Claude? Set up PubChem in Claude and other AIs

See all the AI clients this connector works with ↑

Who it's for

Built for the work PubChem owners hand off.

This MCP is built for professionals working in chemical and biological research who need to move data from databases to their AI workflows.

  • 01

    Medicinal Chemists

    They hand off the task of retrieving molecular properties and drug-like characteristics for lead compounds to their agent.

  • 02

    Pharmacy Students

    They use the agent to quickly look up drug structures and formulas during study sessions.

  • 03

    Biochemistry Researchers

    They delegate the identification of compounds by formula and metabolite exploration to their AI client.

FAQ

Questions PubChem owners ask.

  • 01

    Do I need a PubChem API key to use this MCP?

    No. This MCP handles the connection so you can start searching immediately without managing API credentials.

  • 02

    Which AI clients can use this PubChem MCP?

    Any MCP-compatible client, including Claude, Cursor, Windsurf, and VS Code, can use this connector.

  • 03

    How many compounds can the agent search through?

    The agent has access to over 116 million indexed chemical compounds.

  • 04

    Can I search for compounds using just a formula?

    Yes. The search_pubchem_formula capability allows your agent to find all compounds matching a specific molecular formula.

  • 05

    What kind of chemical data can my agent retrieve?

    Your agent can retrieve molecular weight, SMILES, InChI, XLogP, hydrogen bond donors/acceptors, and complexity.

  • 06

    Do I need an API key to use PubChem?

    No. PubChem PUG REST is completely free and open without any authentication. The only limitation is a rate limit of 5 requests per second and 400 requests per minute, which is more than sufficient for conversational AI usage.

  • 07

    What molecular properties are returned for each compound?

    Each compound includes: CID, IUPAC name, molecular formula, molecular weight, canonical SMILES, InChI identifier, XLogP (lipophilicity), hydrogen bond donor count, hydrogen bond acceptor count, and molecular complexity score. These cover Lipinski's Rule of Five for drug-likeness assessment.

  • 08

    Can I search by molecular formula instead of name?

    Yes! Use the formula search capability with standard notation (e.g., C8H10N4O2 for caffeine, C9H8O4 for aspirin, H2O for water). PubChem will return all compounds matching that exact formula with their names and properties.

Explore

More in The Unthinkable

Suggestions

Connect PubChem to Claude, Cursor, ChatGPT & more