Interpro vs Filesystem
A side-by-side look at the Interpro and Filesystem MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.
Verdict: choose Interpro for biology & bioinformatics work as a local process; choose Filesystem for file systems as a local process. You can also run both side by side in one mcpServers block.
Which MCP server should you choose?
Choose Interpro when
- You need dedicated capabilities in the Biology & Bioinformatics domain.
- You prefer a local stdio subprocess transport.
- You want tools like
search_entries, get_entry, entries_for_protein.
Choose Filesystem when
- You need dedicated capabilities in the File Systems domain.
- You prefer a local stdio subprocess transport.
- Its auth model fits you: No auth required.
- You want tools like
path, head, tail.
Feature & specification comparison
Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Biology & Bioinformatics | File Systems |
| Quality signal | 53/100 · Good | 85/100 · Excellent |
| Install command | Confirmed | Confirmed |
| Transport | Local subprocess (stdio) | Local subprocess (stdio) |
| Auth | Not declared | No auth required |
| Pricing | Not declared | Free |
| Required env vars | None listed | None listed |
| Verified owner | Community listing | Verified |
| GitHub stars | 0 | 91,546 |
| Directory activity | 2 views 0 installs 0 upvotes | 11 views 0 installs 0 upvotes |
| Tools | 3 | 17 |
| Full listing | View Interpro | View Filesystem |
Tools & capabilities
Interpro tools 3
search_entriesSearch 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_entryGet 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_proteinList 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.
Filesystem tools 17
pathheadtailpathscontenteditsoldTextnewTextdryRunsortBysourcedestination- +5 more on the listing page
Ready-to-paste client configs
Paste either block (or both) into your client config, e.g. claude_desktop_config.json or ~/.cursor/mcp.json. We only show a config when the install command is confirmed.
Interpro
{
"mcpServers": {
"interpro": {
"command": "npx",
"args": [
"-y",
"@pipeworx/mcp-interpro"
]
}
}
}
Filesystem
{
"mcpServers": {
"filesystem": {
"command": "npx",
"args": [
"-y",
"@modelcontextprotocol/server-filesystem"
]
}
}
}
Frequently asked questions
Interpro is categorized under Biology & Bioinformatics and uses a local stdio subprocess. Filesystem belongs to File Systems and uses a local stdio subprocess. Pick Interpro for biology & bioinformatics work and Filesystem for file systems.
Copy the mcpServers block from the config section on this page into your client's config (for example claude_desktop_config.json or ~/.cursor/mcp.json), then fully restart the client.
Interpro has no declared pricing — check the project's own site. Filesystem is listed as free. Auth: no auth required. If a server needs environment variables such as API keys, define them under the env key in your client's MCP config.
Yes. MCP clients support multiple servers: add interpro and filesystem as separate keys in the same mcpServers object, and your assistant will call tools from either one.
On AllMCPs, Interpro has a quality signal of 53/100 (Good) with 2 views, 0 installs and 0 GitHub stars. Filesystem has 85/100 (Excellent) with 11 views, 0 installs and 91,546 GitHub stars.