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Connect Pubchem Pug Rest API 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. Bring authoritative molecular data directly into your AI workflow.

Ask AI about this Connector

Developed, maintained, and hosted by Vinkius.

MCP VERIFIED · PRODUCTION READY · VINKIUS GUARANTEED

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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 · 4 capabilities

We ship only the actions that matter.

Capability set01 / 01

01-04

4 capabilities in this set.

Part of 4 available through PubChem.

  1. 01

    Get compound by cid

    This capability pulls full technical details for a specific chemical compound using its unique CID.

  2. 02

    Search compound cids

    Use this to find matching Compound Identifiers (CIDs) by providing a compound name or specific keyword.

  3. 03

    Check API status

    This capability checks if the PubChem PUG REST service is currently online and responding.

  4. 04

    Get compound by name

    This capability retrieves comprehensive chemical data by searching for a compound's name.

Real work

What teams actually run

01

Rapid Compound Auditing

Quickly verify the properties of a list of chemicals by having your agent query CIDs in bulk.

02

Pharmacological Research

Use the AI to identify molecular patterns and verify compound details during drug studies.

03

Data Classification

Query molecular formulas to assist in the deep-dive classification of chemical archives.

04

Workflow Automation

Automate the retrieval of technical metadata for large-scale chemical datasets.

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

915ms average. Fast in production.

PubChem is checked daily against the live service.

Daily averagePeak 1066ms
Oct 3Today
Fastest day
709ms
Slowest day
1066ms
14-day trend
Slowing+9%

Connect your client

One URL. Every client.

Activate the Connector, copy your link, and paste it into the client you already use. 4 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_39PvvjDIh0Gw5sIiVCJqmFBNo6SJy2fu1ixaSd7V/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-pug-rest-api-mcp": {
      "url": "https://edge.vinkius.com/vk_preview_39PvvjDIh0Gw5sIiVCJqmFBNo6SJy2fu1ixaSd7V/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 life sciences and chemical research who need to bridge the gap between raw data and AI-driven analysis.

  • 01

    Scientists and Researchers

    They use the agent to monitor chemical data and pull official metadata.

  • 02

    Pharmacologists

    They hand off the task of auditing molecular patterns and verifying compound details to the AI.

  • 03

    Operations Leads

    They automate scientific data querying to manage research teams more effectively.

FAQ

Questions PubChem owners ask.

  • 01

    Do I need an API key for PubChem?

    No, PubChem is a free and open service, so no API key is required to use this MCP.

  • 02

    Which AI clients can use this MCP?

    You can use this with any MCP-compatible client, including Claude, Cursor, and Windsurf.

  • 03

    How do I find a compound if I only have its name?

    You can use the search_compound_cids capability to find the correct identifier using a name or keyword.

  • 04

    Can I check if the PubChem service is down?

    Yes, the check_api_status capability allows your agent to verify if the PubChem PUG REST service is operational.

  • 05

    Where does the chemical data come from?

    All data is pulled from the authoritative PubChem database provided by the National Library of Medicine.

  • 06

    Is an API Key required for PubChem API?

    No. PubChem is a free and open service provided by the NIH. This server works out of the box without any static credentials required.

  • 07

    What is a CID?

    CID stands for Compound Identifier. It is a unique numerical ID assigned to each chemical compound in the PubChem database.

  • 08

    Can the agent show molecular formulas?

    Yes. The compound details retrieved by your agent include the molecular formula and IUPAC name metadata where available.

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