What is the key difference between Uniprot and Wikipathways?

Uniprot belongs to the Databases category with local stdio execution, while Wikipathways belongs to the Databases category with local stdio execution.

How do I install Uniprot or Wikipathways in Claude Desktop or Cursor?

Copy the mcpServers JSON configuration snippet provided on this page into your claude_desktop_config.json or ~/.cursor/mcp.json file and restart your AI client.

Are Uniprot and Wikipathways free or paid?

Uniprot operates under a Free / Open Source model (No auth required). Wikipathways operates under a Free / Open Source model (No auth required).

Which MCP server has more tools and community activity?

Uniprot lists 0 tools with 0 views and 0 GitHub stars. Wikipathways lists 0 tools with 0 views and 0 GitHub stars.

Can I use both Uniprot and Wikipathways together in the same MCP host?

Yes! MCP hosts like Claude Desktop, Cursor, Windsurf, Cline, and VS Code support configuring multiple servers under the mcpServers object simultaneously.

Side-by-Side Model Context Protocol Comparison

Uniprot vs Wikipathways

In-depth architectural comparison of the Uniprot and Wikipathways MCP servers. Compare execution transports, security boundaries, tool capabilities, quality scores, and ready-to-paste client installation snippets for Claude, Cursor, Windsurf, and VS Code.

At a Glance & Executive Verdict

Uniprot

Databases · Local stdio

Quality: 32/100 (Emerging) | Auth: No auth required

Wikipathways

Databases · Local stdio

Quality: 28/100 (Emerging) | Auth: No auth required

Verdict Summary: Choose Uniprot if you need specialized Databases tools running via a local process. Choose Wikipathways if your workspace requires Databases integration with local subprocess execution. Both servers can be configured concurrently in your client's mcpServers manifest.

Which MCP Server Should You Choose?

Choose Uniprot when:

You need dedicated capabilities in the Databases domain.
You prefer local stdio subprocess transport architecture.
Your security boundary fits: No auth required (Free / Open Source).

Explore Uniprot Details

Choose Wikipathways when:

You need dedicated capabilities in the Databases domain.
You prefer local stdio subprocess transport architecture.
Your security boundary fits: No auth required (Free / Open Source).

Explore Wikipathways Details

Feature & Specification Comparison

Specification	U Uniprot Databases	Wikipathways Databases
Summary	UniProt MCP — protein sequence + function database.	WikiPathways MCP — open community pathway database.
Category & Scope	Databases	Databases
Quality signal

Tools & Capabilities Breakdown

Uniprot Tools (0)

No explicit tool names declared in metadata yet. Check project README on main listing page.

Wikipathways Tools (0)

No explicit tool names declared in metadata yet. Check project README on main listing page.

Ready-to-Paste Client Configurations

Paste either (or both) of these JSON server blocks into your client config file (e.g. claude_desktop_config.json or ~/.cursor/mcp.json).

Uniprot Configuration

mcpServers (Claude Desktop / Cursor)

{
  "mcpServers": {
    "uniprot": {
      "command": "npx",
      "args": [
        "-y",
        "uniprot"
      ]
    }
  }
}

Wikipathways Configuration

mcpServers (Claude Desktop / Cursor)

{
  "mcpServers": {
    "wikipathways": {
      "command": "npx",
      "args": [
        "-y",
        "wikipathways"
      ]
    }
  }
}

Frequently Asked Questions

Uniprot is categorized under Databases and uses a local stdio subprocess. In contrast, Wikipathways belongs to Databases using local stdio subprocess. Select Uniprot when you need capabilities focused on databases and Wikipathways when you require tools for databases.

More alternatives to Uniprot More alternatives to Wikipathways Databases category hub