Protein MCP Server vs Filesystem
A side-by-side look at the Protein MCP Server 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 Protein MCP Server for biology & bioinformatics work; 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 Protein MCP Server when
- You need dedicated capabilities in the Biology & Bioinformatics domain.
- Its auth model fits you: No auth required.
- You want tools like
protein_search_structures, protein_get_structure, protein_find_similar.
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 | 49/100 · Fair | 85/100 · Excellent |
| Install command | Not confirmed yet | Confirmed |
| Transport | — | Local subprocess (stdio) |
| Auth | No auth required | No auth required |
| Pricing | Free | Free |
| Required env vars | None listed | None listed |
| Verified owner | Community listing | Verified |
| GitHub stars | 6 | 91,546 |
| Directory activity | 1 views 0 installs 0 upvotes | 11 views 0 installs 0 upvotes |
| Tools | 7 | 17 |
| Full listing | View Protein MCP Server | View Filesystem |
Tools & capabilities
Protein MCP Server tools 7
protein_search_structuresSearch experimental and predicted structures by text, sequence, or organism/method/resolution, with optional facetsprotein_get_structureFetch metadata and coordinate URLs for experimental, predicted, or best-available structuresprotein_find_similarFind sequence homologs (RCSB mmseqs2) or fold homologs (Foldseek)protein_track_ligandsResolve ligands to component IDs, find structures containing one, or map its binding siteprotein_compare_structuresAlign structures with TM-align or jFATCAT, against a reference or all pairsprotein_analyze_collectionProfile the PDB as counts, histograms, timelines, and cross-tabsprotein_get_annotationsFetch UniProt features and variants plus InterPro domains with GO terms
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.
Protein MCP Server
No confirmed install command for Protein MCP Server yet — follow the setup steps linked from its listing page rather than a guessed package name.
Filesystem
{
"mcpServers": {
"filesystem": {
"command": "npx",
"args": [
"-y",
"@modelcontextprotocol/server-filesystem"
]
}
}
}
Frequently asked questions
Protein MCP Server is categorized under Biology & Bioinformatics and uses an install path we have not confirmed yet. Filesystem belongs to File Systems and uses a local stdio subprocess. Pick Protein MCP Server 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. Protein MCP Server has no confirmed install command yet — follow its own setup instructions.
Protein MCP Server is listed as free. Auth: no auth required. 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 protein-mcp-server and filesystem as separate keys in the same mcpServers object, and your assistant will call tools from either one.
On AllMCPs, Protein MCP Server has a quality signal of 49/100 (Fair) with 1 views, 0 installs and 6 GitHub stars. Filesystem has 85/100 (Excellent) with 11 views, 0 installs and 91,546 GitHub stars.