What is the key difference between Alphafold and Interpro?

Alphafold belongs to the Biology & Bioinformatics category with local stdio execution, while Interpro belongs to the Biology & Bioinformatics category with local stdio execution.

How do I install Alphafold or Interpro 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 Alphafold and Interpro free or paid?

Alphafold operates under a Free / Open Source model (No auth required). Interpro operates under a Free / Open Source model (No auth required).

Which MCP server has more tools and community activity?

Alphafold lists 1 tools with 0 views and 0 GitHub stars. Interpro lists 3 tools with 0 views and 0 GitHub stars.

Can I use both Alphafold and Interpro 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

Alphafold vs Interpro

In-depth architectural comparison of the Alphafold and Interpro 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

Alphafold

Biology & Bioinformatics · Local stdio

Quality: 43/100 (Fair) | Auth: No auth required

Interpro

Biology & Bioinformatics · Local stdio

Quality: 44/100 (Fair) | Auth: No auth required

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

Which MCP Server Should You Choose?

Choose Alphafold when:

You need dedicated capabilities in the Biology & Bioinformatics domain.
You prefer local stdio subprocess transport architecture.
Your security boundary fits: No auth required (Free / Open Source).
Primary tools included: prediction.

Explore Alphafold Details

Choose Interpro when:

You need dedicated capabilities in the Biology & Bioinformatics domain.
You prefer local stdio subprocess transport architecture.
Your security boundary fits: No auth required (Free / Open Source).
Primary tools included: search_entries, get_entry, entries_for_protein.

Explore Interpro Details

Feature & Specification Comparison

Specification	A Alphafold Biology & Bioinformatics	I Interpro Biology & Bioinformatics
Summary	AlphaFold DB MCP — predicted protein structures.	InterPro MCP (EBI) — protein family / domain / functional-site classification.
Category & Scope	Biology & Bioinformatics	Biology & Bioinformatics
Quality signal

Tools & Capabilities Breakdown

Alphafold Tools (1)

prediction

Interpro Tools (3)

search_entries

Search InterPro for protein families, domains, repeats and functional sites by keyword (text search over entry names/accessions). InterPro is EBI's integrated protein-signature classification (Pfam, PROSITE, SMART, CDD, PANTHER, ...). Returns matching entries with accession (IPRxxxxxx), name, type…

get_entry

Get full details for a single InterPro entry by accession (e.g. "IPR000001"). Returns the entry name, type, a plain-text description, member-signature/protein counters, and associated GO terms (molecular function / biological process / cellular component). Use after search_entries or entries_for_pr…

entries_for_protein

List all InterPro entries (families, domains, sites) found on a given UniProt protein, by UniProt accession (e.g. "P12345"). Returns each matching InterPro signature with accession, name and type. Useful to functionally annotate a protein. Complements UniProt/AlphaFold. Keyless.

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).

Alphafold Configuration

mcpServers (Claude Desktop / Cursor)

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

Interpro Configuration

mcpServers (Claude Desktop / Cursor)

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

Frequently Asked Questions

Alphafold is categorized under Biology & Bioinformatics and uses a local stdio subprocess. In contrast, Interpro belongs to Biology & Bioinformatics using local stdio subprocess. Select Alphafold when you need capabilities focused on biology & bioinformatics and Interpro when you require tools for biology & bioinformatics.

More alternatives to Alphafold More alternatives to Interpro Biology & Bioinformatics category hub