Filesystem vs Pdbe
A side-by-side look at the Filesystem and Pdbe MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.
Verdict: choose Filesystem for file systems work as a local process; choose Pdbe for biology & bioinformatics as a local process. You can also run both side by side in one mcpServers block.
Which MCP server should you choose?
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.
Choose Pdbe when
- You need dedicated capabilities in the Biology & Bioinformatics domain.
- You prefer a local stdio subprocess transport.
- You want tools like
get_summary, get_molecules, uniprot_mappings.
Feature & specification comparison
Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | File Systems | Biology & Bioinformatics |
| Quality signal | 85/100 · Excellent | 51/100 · Good |
| Install command | Confirmed | Confirmed |
| Transport | Local subprocess (stdio) | Local subprocess (stdio) |
| Auth | No auth required | Not declared |
| Pricing | Free | Not declared |
| Required env vars | None listed | None listed |
| Verified owner | Verified | Community listing |
| GitHub stars | 91,512 | 0 |
| Directory activity | 11 views 0 installs 0 upvotes | 3 views 0 installs 0 upvotes |
| Tools | 17 | 3 |
| Full listing | View Filesystem | View Pdbe |
Tools & capabilities
Filesystem tools 17
pathheadtailpathscontenteditsoldTextnewTextdryRunsortBysourcedestination- +5 more on the listing page
Pdbe tools 3
get_summaryPDBe (Protein Data Bank in Europe, EBI): get a PDB entry summary — title, experimental method, release date, source organism, and entity counts (polypeptide/ligand/water/...). Keyless. The EBI counterpart to RCSB PDB. Pass a 4-char PDB id like "1cbs".get_moleculesPDBe (EBI): list the molecules/entities in a PDB structure — proteins, nucleic acids, and ligands, each with entity_id, molecule_type, name, and chain length. Keyless. Pass a 4-char PDB id like "1cbs".uniprot_mappingsPDBe (EBI): SIFTS cross-database mapping of a PDB structure to UniProt — for each UniProt accession, the matching chains and residue range. Curated cross-database mappings unique to EBI. Keyless. Pass a 4-char PDB id like "1cbs".
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.
Filesystem
{
"mcpServers": {
"filesystem": {
"command": "npx",
"args": [
"-y",
"@modelcontextprotocol/server-filesystem"
]
}
}
}
Pdbe
{
"mcpServers": {
"pdbe": {
"command": "npx",
"args": [
"-y",
"@pipeworx/mcp-pdbe"
]
}
}
}
Frequently asked questions
Filesystem is categorized under File Systems and uses a local stdio subprocess. Pdbe belongs to Biology & Bioinformatics and uses a local stdio subprocess. Pick Filesystem for file systems work and Pdbe for biology & bioinformatics.
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.
Filesystem is listed as free. Auth: no auth required. Pdbe has no declared pricing — check the project's own site. 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 filesystem and pdbe as separate keys in the same mcpServers object, and your assistant will call tools from either one.
On AllMCPs, Filesystem has a quality signal of 85/100 (Excellent) with 11 views, 0 installs and 91,512 GitHub stars. Pdbe has 51/100 (Good) with 3 views, 0 installs and 0 GitHub stars.