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.

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.

Can I search by molecular formula instead of name?

Yes! Use the formula search tool 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.

PubChem MCP Server for Windsurf 3 tools — connect in under 2 minutes

Name: PubChem
Availability: InStock
Author: Vinkius

docs.windsurf.com/windsurf/mcp

Built by Vinkius GDPR 3 Tools IDE

Windsurf brings agentic AI coding to a purpose-built IDE. Connect PubChem through Vinkius and Cascade will auto-discover every tool. ask questions, generate code, and act on live data without leaving your editor.

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ASK AI ABOUT THIS MCP SERVER

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Vinkius supports streamable HTTP and SSE.

RecommendedModern Approach — Zero Configuration

Vinkius Desktop App

The modern way to manage MCP Servers — no config files, no terminal commands. Install PubChem and 2,500+ MCP Servers from a single visual interface.

Download Free Open SourceNo signup required

Classic Setup·json

{
  "mcpServers": {
    "pubchem": {
      "url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
    }
  }
}

Fully ManagedVinkius Servers

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IAMAccess control

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DLPData protection

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* Every MCP server runs on Vinkius-managed infrastructure inside AWS - a purpose-built runtime with per-request V8 isolates, Ed25519 signed audit chains, and sub-40ms cold starts optimized for native MCP execution. See our infrastructure

About PubChem MCP Server

Connect your AI agent to PubChem — the world's largest open chemistry database, maintained by the National Center for Biotechnology Information (NCBI/NIH).

Windsurf's Cascade agent chains multiple PubChem tool calls autonomously. query data, analyze results, and generate code in a single agentic session. Paste Vinkius Edge URL, reload, and all 3 tools are immediately available. Real-time tool feedback appears inline, so you see API responses directly in your editor.

What you can do

Compound Search — Find chemical compounds by common name (aspirin, caffeine, glucose), IUPAC name, or CAS number across 116M+ indexed compounds
CID Lookup — Get comprehensive molecular data for any compound by its PubChem Compound ID including formula, weight, SMILES, InChI, and physicochemical properties
Formula Search — Find all compounds matching a specific molecular formula (e.g., C9H8O4 for aspirin)

The PubChem MCP Server exposes 3 tools through the Vinkius. Connect it to Windsurf in under two minutes — no API keys to rotate, no infrastructure to provision, no vendor lock-in. Your configuration, your data, your control.

How to Connect PubChem to Windsurf via MCP

Follow these steps to integrate the PubChem MCP Server with Windsurf.

Open MCP Settings

Go to Settings → MCP Configuration or press Cmd+Shift+P and search "MCP"

Add the server

Paste the JSON configuration above into mcp_config.json

Save and reload

Windsurf will detect the new server automatically

Start using PubChem

Open Cascade and ask: "Using PubChem, help me...". 3 tools available

Why Use Windsurf with the PubChem MCP Server

Windsurf provides unique advantages when paired with PubChem through the Model Context Protocol.

Windsurf's Cascade agent autonomously chains multiple tool calls in sequence, solving complex multi-step tasks without manual intervention

Purpose-built for agentic workflows. Cascade understands context across your entire codebase and integrates MCP tools natively

JSON-based configuration means zero code changes: paste a URL, reload, and all 3 tools are immediately available

Real-time tool feedback is displayed inline, so you see API responses directly in your editor without switching contexts

PubChem + Windsurf Use Cases

Practical scenarios where Windsurf combined with the PubChem MCP Server delivers measurable value.

Automated code generation: ask Cascade to fetch data from PubChem and generate models, types, or handlers based on real API responses

Live debugging: query PubChem tools mid-session to inspect production data while debugging without leaving the editor

Documentation generation: pull schema information from PubChem and have Cascade generate comprehensive API docs automatically

Rapid prototyping: combine PubChem data with Cascade's code generation to scaffold entire features in minutes

PubChem MCP Tools for Windsurf (3)

These 3 tools become available when you connect PubChem to Windsurf via MCP:

get_pubchem_compound

Get full chemical data for a PubChem compound by CID

search_pubchem

Returns molecular formula, weight, SMILES, InChI, XLogP, hydrogen bond donors/acceptors, and complexity. Try: aspirin, caffeine, glucose, penicillin, dopamine. Search PubChem for chemical compounds by name

search_pubchem_formula

g. C9H8O4, C8H10N4O2, H2O) and find matching compounds. Find compounds by molecular formula

Example Prompts for PubChem in Windsurf

Ready-to-use prompts you can give your Windsurf agent to start working with PubChem immediately.

"What are the molecular properties of aspirin?"

"Search for compounds with the molecular formula C8H10N4O2."

"Get the full chemical details for PubChem compound CID 5090."

Troubleshooting PubChem MCP Server with Windsurf

Common issues when connecting PubChem to Windsurf through the Vinkius, and how to resolve them.

Server not connecting

Check Settings → MCP for the server status. Try toggling it off and on.

PubChem + Windsurf FAQ

Common questions about integrating PubChem MCP Server with Windsurf.

How does Windsurf discover MCP tools?

Windsurf reads the mcp_config.json file on startup and connects to each configured server via Streamable HTTP. Tools are listed in the MCP panel and available to Cascade automatically.

Can Cascade chain multiple MCP tool calls?

Yes. Cascade is an agentic system. it can plan and execute multi-step workflows, calling several tools in sequence to accomplish complex tasks without manual prompting between steps.

Does Windsurf support multiple MCP servers?

Yes. Add as many servers as needed in mcp_config.json. Each server's tools appear in the MCP panel and Cascade can use tools from different servers in a single flow.