UniProt MCP Server for Windsurf 3 tools — connect in under 2 minutes
Windsurf brings agentic AI coding to a purpose-built IDE. Connect UniProt 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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Vinkius supports streamable HTTP and SSE.
Vinkius Desktop App
The modern way to manage MCP Servers — no config files, no terminal commands. Install UniProt and 2,500+ MCP Servers from a single visual interface.
{
"mcpServers": {
"uniprot": {
"url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
}
}
}
* 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 UniProt MCP Server
Connect your AI agent to UniProt — the Universal Protein Resource — the world's definitive knowledge base for protein sequence and functional information.
Windsurf's Cascade agent chains multiple UniProt 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
- Protein Search — Find proteins by name, gene symbol, function, or organism across 250M+ entries from both TrEMBL (auto-annotated) and Swiss-Prot (manually curated)
- Accession Lookup — Get complete protein data by UniProt accession number (e.g., P04637 for human p53) including function, subcellular location, and full amino acid sequence
- Gene Search — Find all proteins encoded by a specific gene name across multiple organisms to compare orthologs and paralogs
The UniProt 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 UniProt to Windsurf via MCP
Follow these steps to integrate the UniProt 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 UniProt
Open Cascade and ask: "Using UniProt, help me...". 3 tools available
Why Use Windsurf with the UniProt MCP Server
Windsurf provides unique advantages when paired with UniProt 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
UniProt + Windsurf Use Cases
Practical scenarios where Windsurf combined with the UniProt MCP Server delivers measurable value.
Automated code generation: ask Cascade to fetch data from UniProt and generate models, types, or handlers based on real API responses
Live debugging: query UniProt tools mid-session to inspect production data while debugging without leaving the editor
Documentation generation: pull schema information from UniProt and have Cascade generate comprehensive API docs automatically
Rapid prototyping: combine UniProt data with Cascade's code generation to scaffold entire features in minutes
UniProt MCP Tools for Windsurf (3)
These 3 tools become available when you connect UniProt to Windsurf via MCP:
get_uniprot_protein
Get full protein details by UniProt accession ID
search_uniprot
Returns protein name, gene, organism, function, subcellular location, and sequence. Try: insulin, hemoglobin, p53, BRCA1, spike protein. Search UniProt for proteins by name, function, or keyword
search_uniprot_gene
Returns all protein isoforms and their functional annotations. Find proteins encoded by a specific gene
Example Prompts for UniProt in Windsurf
Ready-to-use prompts you can give your Windsurf agent to start working with UniProt immediately.
"Tell me about the p53 tumor suppressor protein and its function."
"Find all proteins encoded by the BRCA1 gene."
"Look up UniProt accession Q9BYF1 and show me its full details."
Troubleshooting UniProt MCP Server with Windsurf
Common issues when connecting UniProt to Windsurf through the Vinkius, and how to resolve them.
Server not connecting
UniProt + Windsurf FAQ
Common questions about integrating UniProt MCP Server with Windsurf.
How does Windsurf discover MCP tools?
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?
Does Windsurf support multiple MCP servers?
mcp_config.json. Each server's tools appear in the MCP panel and Cascade can use tools from different servers in a single flow.Connect UniProt with your favorite client
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Connect UniProt to Windsurf
Get your token, paste the configuration, and start using 3 tools in under 2 minutes. No API key management needed.