Rcsb Pdb
NPM · @PIPEWORX/MCP-RCSB-PDB · 2 COMPONENTS
RCSB PDB MCP — experimentally determined macromolecular structures.
Available components
Last scanned (3 hours ago)
Scores higher than 58% of npm servers
Category Health and Science
How this component scores in each security and reliability category. Every signal is checked automatically from public evidence about the published package, including repeated runs of it in an isolated sandbox, and we only credit what we can confirm. How we score → Why this is hard to score →
Supply Chain Security100
- No malware found by supply-chain analysis.Pass
- No known CVEs affecting this package version or its production dependencies.Pass
- No install/post-install scripts declared.Pass
- No production dependencies, so there is no dependency health to assess. View diagnostics → Pass
Provenance & Transparency97
- Source repository is publicly reachable at the declared URL. View diagnostics → Pass
- Cryptographically verified build provenance (signed, bound to pipeworx-io/mcp-rcsb-pdb). View diagnostics → Pass
- Clear OSI-approved license (MIT).Pass
- Actively maintained (last published 0 days ago).Pass
- Disclosure check failed: no security disclosure policy was found in the source repository. See how to fix → Fail
Schema Quality & AI Usability69
- AI-judged instruction clarity (good).Pass
- Tool/resource definitions use about 683 tokens (~113/item across 6 items; 6 tools + 0 resources), lean.Pass
- Usage-examples check failed: none of the tools include examples. See how to fix → Fail
Stability & Change Management3
- Stability observed for 1 of 30 days with no destabilising changes; credit accrues until the full window elapses.Partial
Tool Coverage76
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 27% of tool parameters carry a description.Partial
Tool Safety100
- No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.Pass
- We read all 6 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 7 captured unit(s) of tool text and found none that tries to manipulate the model reading it.Pass
Capabilities100
- Implements a supported MCP spec version (2025-11-25); the latest is 2026-07-28.Pass
Every change we have recorded for this component, newest first. Security-relevant changes are always shown. ▲ marks a change for the better, ▼ a change for the worse; unmarked changes are neutral.
- 4 Nov 26 78
First indexed and scored.
Diagnostic detail from the automated scan of this channel: what the scanner observed at each step, so you can see exactly where a check passed or failed. It is informational only and never changes the trust score.
Captured 5 Nov 2026 · Analysed npm/@pipeworx/mcp-rcsb-pdb@0.2.1
Provenance Verified
A signed build attestation was found and verified, binding this exact artifact to the source repository it claims to come from.
| Result | Verified |
|---|---|
| Ecosystem | npm |
| Reason | Verified |
| Discovered via | Registry attestation endpoint |
| Source repo | pipeworx-io/mcp-rcsb-pdb |
| Certificate issuer | https://token.actions.githubusercontent.com |
| Certificate SAN | https://github.com/pipeworx-io/mcp-rcsb-pdb/.github/workflows/publish.yml@refs/heads/main |
| Rekor log index | 3691875587 |
| Predicate type | SLSA build provenance https://slsa.dev/provenance/v1 |
| Subject digest | sha512:342e34c197619613a88bf58b208ee16b1aa891b5166049cc0a3cea1d2dc14e29e75dbe8639bd2ba0669188eaf54beb0f5bca8808e75b19d99e9e0f844 |
Background: How many MCP packages publish verified provenance →
Dependencies 0 packages
| Packages resolved | 0 |
|---|---|
| Tree resolution | Complete |
Background: SBOMs and build attestations, explained →
The tools this component advertises to a client, with an estimated token cost for each. Expand a tool to see its parameters and schema. The per-tool counts are indicative and are not scored directly; the schema's total context footprint is one signal in Schema Quality & AI Usability. A tool's description is untrusted text the model reads on every call, which is what makes this list a security surface and not just an inventory: how tool poisoning works →
assembly ~94
"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.
| Name | Type | Req | Description |
|---|---|---|---|
| assembly_id | string | – | – |
| pdb_id | string | yes | – |
No output schema declared.
No examples provided.
ligand ~95
"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.
| Name | Type | Req | Description |
|---|---|---|---|
| ligand_id | string | yes | – |
| pdb_id | string | yes | – |
No output schema declared.
No examples provided.
polymer_entity ~95
"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.
| Name | Type | Req | Description |
|---|---|---|---|
| entity_id | string | yes | – |
| pdb_id | string | yes | – |
No output schema declared.
No examples provided.
search ~166
"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.
| Name | Type | Req | Description |
|---|---|---|---|
| limit | number | – | 1-1000 (default 25). |
| query | string | yes | Free-text, e.g. "CRISPR Cas9". |
| return_type | string | – | entry (default) | polymer_entity | non_polymer_entity | assembly |
No output schema declared.
No examples provided.
structure ~106
"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.
| Name | Type | Req | Description |
|---|---|---|---|
| pdb_id | string | yes | – |
No output schema declared.
No examples provided.
summary ~69
Lightweight 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`.
| Name | Type | Req | Description |
|---|---|---|---|
| pdb_id | string | yes | – |
No output schema declared.
No examples provided.
How do I install the Rcsb Pdb MCP server?
Rcsb Pdb runs locally as an npm package, launched with npx -y @pipeworx/mcp-rcsb-pdb. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.
npm · @pipeworx/mcp-rcsb-pdb
claude mcp add pipeworx-io-rcsb-pdb -- npx -y @pipeworx/mcp-rcsb-pdb
What is the Rcsb Pdb MCP server?
Rcsb Pdb is an MCP server listed in the public MCP registry as io.github.pipeworx-io/rcsb-pdb. RCSB PDB MCP, experimentally determined macromolecular structures. This page covers its npm package (@pipeworx/mcp-rcsb-pdb).
Is the Rcsb Pdb MCP server safe to use?
Rcsb Pdb scores 78 out of 100 on VerifyMCP. We found no known CVEs affecting it as of 5 November 2026. It declares no install or post-install scripts. Its build provenance is signed and verified. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.
What tools does the Rcsb Pdb MCP server expose?
Rcsb Pdb exposes 6 tools: search, structure, polymer_entity, ligand, assembly, summary. Their descriptions and schemas cost roughly 625 tokens of context every time the server is loaded.
Is the Rcsb Pdb MCP server still maintained?
Rcsb Pdb is still listed as active in the MCP registry. We last reached this channel on 5 November 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.
What licence is the Rcsb Pdb MCP server under?
Rcsb Pdb declares the MIT licence, which is OSI-approved. That covers the source only, and says nothing about the cost of any service it calls.