Rcsb Pdb vs Filesystem
A side-by-side look at the Rcsb Pdb 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 Rcsb Pdb 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 Rcsb Pdb when
- You need dedicated capabilities in the Biology & Bioinformatics domain.
- You prefer a local stdio subprocess transport.
- You want tools like
search, structure, polymer_entity.
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 | 59/100 · 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 | 1 views 0 installs 0 upvotes | 11 views 0 installs 0 upvotes |
| Tools | 6 | 17 |
| Full listing | View Rcsb Pdb | View Filesystem |
Tools & capabilities
Rcsb Pdb tools 6
search"Find protein structure of [target]" / "search PDB for [protein]" / "is there a crystal structure of [X]" / "[disease target] structures" / "CRISPR / kinase / GPCR structures" — text search the RCSB PDB (the global archive of experimentally-determined 3D protein/RNA/DNA structures). Returns matching PDB IDs you can pass to `structure` or `summary`. Use for structural biology, drug design, protein characterization.structure"PDB entry [1abc] details" / "fetch protein structure [pdb_id]" / "metadata for [PDB ID]" — full PDB entry record by ID (e.g. "1abc", "7BV2"). Returns experimental method (X-ray / cryo-EM / NMR), resolution, authors, deposition date, organism, ligands, related entities. Use after `search` to inspect a specific structure.polymer_entity"Chain [N] of PDB [ID]" / "sequence of chain in [pdb_id]" — fetch the polymer-entity (protein/DNA/RNA chain) metadata for a specific PDB entry. Returns sequence, source organism, UniProt cross-references, GO annotations. Use to drill into one chain of a multi-chain structure.ligand"Ligand / cofactor / drug bound to [pdb_id]" / "small molecule in [PDB entry]" — fetch a non-polymer ligand record (small molecule, cofactor, ion, or bound drug) for a PDB entry. Use to inspect what's bound in a co-crystal structure — common in drug discovery / SBDD.assembly"Biological assembly of [pdb_id]" / "functional oligomer for [PDB entry]" — fetch a biological assembly record (the functional oligomeric unit, which often differs from the crystallographic asymmetric unit). Use when you need the actual functional form of a protein (dimer / tetramer / etc.) rather than the crystal contents.summaryLightweight lookup for a PDB entry by 4-char ID: tries the RCSB UniProt endpoint first, falls back to the core entry record. Returns title, experimental method, resolution, and deposition date without the full polymer/ligand detail of `structure`.
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.
Rcsb Pdb
{
"mcpServers": {
"rcsb-pdb": {
"command": "npx",
"args": [
"-y",
"@pipeworx/mcp-rcsb-pdb"
]
}
}
}
Filesystem
{
"mcpServers": {
"filesystem": {
"command": "npx",
"args": [
"-y",
"@modelcontextprotocol/server-filesystem"
]
}
}
}
Frequently asked questions
Rcsb Pdb is categorized under Biology & Bioinformatics and uses a local stdio subprocess. Filesystem belongs to File Systems and uses a local stdio subprocess. Pick Rcsb Pdb 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.
Rcsb Pdb 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 rcsb-pdb and filesystem as separate keys in the same mcpServers object, and your assistant will call tools from either one.
On AllMCPs, Rcsb Pdb has a quality signal of 59/100 (Good) with 1 views, 0 installs and 0 GitHub stars. Filesystem has 85/100 (Excellent) with 11 views, 0 installs and 91,546 GitHub stars.