io.github.cyanheads/protein-mcp-server
NPM · PROTEIN-MCP-SERVER
MCP Server for 3D protein structural data retrieval & analysis from RCSB PDB, PDBe, and UniProt.
Available components
Last scanned (5 hours ago)
Scores higher than 50% 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 Security81
- No malware found by supply-chain analysis.Pass
- CVE check failed: a known high-severity CVE affects @opentelemetry/auto-instrumentations-node 0.64.6, a direct dependency. A fixed version is available. View diagnostics → Fail
- No install/post-install scripts declared.Pass
- Dependency health was assessed across the 400 of 422 dependencies we could resolve, so this covers what we could see, not the whole tree. View diagnostics → Partial
Provenance & Transparency42
- Source repository is publicly reachable at the declared URL. View diagnostics → Pass
- Provenance check failed: no build-provenance attestation is published. See how to fix → View diagnostics → Fail
- Clear OSI-approved license (Apache-2.0).Pass
- Maintenance check failed: the publisher has marked this version as deprecated on the registry, telling users to stop installing it. See how to fix → Fail
- Publishes a security disclosure policy (SECURITY.md).Pass
Schema Quality & AI Usability84
- 100% of prompts and resources have a non-trivial description (not blank, and not just the item's name).Pass
- AI-judged instruction clarity (good).Pass
- Tool/resource definitions use about 856 tokens (~107/item across 8 items; 6 tools + 2 resources), lean.Pass
- Usage-examples check failed: none of the tools include examples. See how to fix → Fail
Stability & Change Management77
- Stability observed for 23 of 30 days with no destabilising changes; credit accrues until the full window elapses.Partial
Tool Coverage100
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 100% of tool parameters carry a description.Pass
- Structured output schemas are declared (100% of tools); any adoption earns full credit.Pass
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
Capabilities60
- Spec-recency check failed: implements MCP spec 2025-06-18; the latest is 2026-07-28. See how to fix → Fail
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.
- 5 Nov 26 −3
- Stability: pass → 0.77 functional
- 31 Oct 26 0
- CVE-2026-118764 affects this package: high ▼ security
- 30 Oct 26 0
- Stability: 0.97 → pass security
- 29 Oct 26 0
- CVE-2026-118663 affects this package: high ▼ security
- Stability: pass → 0.97 functional
- 24 Oct 26 0
- CVE-2023-54404 affects this package: high ▼ security
- 23 Oct 26 0
- Stability: 0.97 → pass security
- 22 Oct 26 0
- Stability: pass → 0.97 functional
- 16 Oct 26 0
- Stability: 0.97 → pass security
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/protein-mcp-server@1.0.3
Provenance No attestation
The registry publishes no build provenance for this version, so there is nothing to verify.
| Result | No attestation |
|---|---|
| Ecosystem | npm |
Background: How many MCP packages publish verified provenance →
Vulnerabilities 10 findings
| ID | CVE | Severity | Vector | Fix available |
|---|---|---|---|---|
| GHSA-rmxm-3fg6-px4f | CVE-2026-118663 | medium | CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:L/I:N/A:N | yes |
| GHSA-q7rr-3cgh-j5r3 | CVE-2026-44902 | high | CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:N/I:N/A:H | yes |
| GHSA-8988-4f7v-96qf | CVE-2026-54285 | medium | CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:N/I:N/A:L | yes |
| GHSA-qqmp-wf37-98f9 | CVE-2026-104872 | medium | CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:C/C:L/I:N/A:N | yes |
| GHSA-45rx-2jwx-cxfr | CVE-2026-59892 | high | CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:N/I:N/A:H | yes |
| GHSA-g3hv-75wg-m249 | CVE-2026-118764 | medium | yes | |
| GHSA-w5hq-g745-h8pq | CVE-2026-41907 | high | CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:N/I:H/A:N | yes |
| GHSA-9965-vmph-33xx | CVE-2025-56200 | medium | CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:C/C:L/I:L/A:N | yes |
| GHSA-vghf-hv5q-vc2g | CVE-2025-12758 | high | CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:N/I:N/A:H | yes |
| GHSA-mrhx-c7xc-m3w5 | CVE-2023-54404 | high | CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:N/I:N/A:H | yes |
Background: What a vulnerability scan can and cannot prove →
Dependencies 400 packages
| Packages resolved | 400 |
|---|---|
| Deprecated | 6 |
| Stale | 93 |
| Tree resolution | Partial |
The dependency tree was only partially resolved, so these counts may be incomplete.
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 →
protein_analyze_collection Analyze Protein Collection ~106
Perform statistical analysis of protein structure database by fold classification, function, organism, or experimental method. Useful for understanding structural biology trends and dataset composition.
| Name | Type | Req | Description |
|---|---|---|---|
| analysisType | string | yes | Type of analysis: fold (structural classification), function, organism, or method. |
| filters | object | – | Filters to narrow analysis scope. |
| groupBy | string | – | Secondary grouping dimension (e.g., year for trends). |
| limit | integer | – | Number of top categories to return. |
| Name | Type | Req | Description |
|---|---|---|---|
| analysisType | string | yes | The type of analysis that was performed. |
| statistics | array | yes | An array of statistical results for the top categories. |
| totalStructures | number | yes | Total number of structures matching the query. |
| trends | array | – | Optional array of trend data, present if `groupBy` was used. |
No examples provided.
protein_compare_structures Compare Protein Structures ~112
Compare multiple protein structures using structural alignment. Calculate RMSD, TM-score, and identify flexible/rigid regions. Useful for analyzing conformational changes and structural similarities.
| Name | Type | Req | Description |
|---|---|---|---|
| alignmentMethod | string | – | Alignment algorithm to use. |
| chainSelections | array | – | Specific chain selections (default: auto-select first chain). |
| includeVisualization | boolean | – | Include PyMOL/ChimeraX visualization script. |
| pdbIds | array | yes | Array of PDB IDs to compare (2-10 structures). |
| Name | Type | Req | Description |
|---|---|---|---|
| alignment | object | yes | Overall alignment statistics. |
| conformationalAnalysis | object | – | Analysis of flexible and rigid structural regions. |
| pairwiseComparisons | array | yes | Pairwise comparison results for all structure pairs. |
| visualization | string | – | Visualization script. |
No examples provided.
protein_find_similar Find Similar Proteins ~127
Find proteins similar to a query by sequence (BLAST) or structure (DALI, FATCAT). Use for homology searches, fold recognition, and evolutionary analysis.
| Name | Type | Req | Description |
|---|---|---|---|
| chainId | string | – | Specific chain ID for structural similarity (default: auto-select first chain "A"). |
| limit | integer | – | Maximum number of results. |
| query | object | yes | Query: PDB ID, FASTA sequence, or structure data. |
| similarityType | string | yes | Type of similarity search: sequence or structure. |
| threshold | object | – | Similarity thresholds for filtering results. |
| Name | Type | Req | Description |
|---|---|---|---|
| query | object | yes | Information about the search query. |
| results | array | yes | Array of similar structures found. |
| similarityType | string | yes | Type of similarity search performed. |
| totalCount | number | yes | Total number of results found. |
No examples provided.
protein_get_structure Get Protein Structure ~160
Retrieve complete 3D structure data for a specific PDB entry including coordinates, experimental metadata, and annotations. Use this after searching to get detailed structural information.
| Name | Type | Req | Description |
|---|---|---|---|
| format | string | – | Structure file format: mmcif (modern, recommended), bcif (binary, efficient), pdb (legacy), pdbml (XML), or json (metadata only). |
| includeAnnotations | boolean | – | Include functional annotations and citations. |
| includeCoordinates | boolean | – | Include 3D coordinate data (disable for metadata-only queries). |
| includeExperimentalData | boolean | – | Include experimental metadata (resolution, R-factors, unit cell). |
| pdbId | string | yes | 4-character PDB identifier (e.g., "1ABC", "2GBP"). |
| Name | Type | Req | Description |
|---|---|---|---|
| annotations | object | yes | Functional annotations and literature references. |
| experimental | object | yes | Experimental metadata. |
| pdbId | string | yes | 4-character PDB identifier. |
| structure | object | yes | Structure coordinate and topology data. |
| title | string | yes | Structure title/description. |
No examples provided.
protein_search_structures Search Protein Structures ~210
Search protein structures from the Protein Data Bank by name, organism, experimental method, or resolution. Returns a paginated list of matching structures with metadata. Use this to discover proteins of interest before fetching detailed structure data.
| Name | Type | Req | Description |
|---|---|---|---|
| experimentalMethod | string | – | Filter by experimental method used to determine the structure. |
| limit | integer | – | Maximum number of results to return (1-100, default 25). |
| maxResolution | number | – | Maximum resolution in Angstroms (e.g., 2.0 for high-resolution structures). |
| minResolution | number | – | Minimum resolution in Angstroms. |
| offset | integer | – | Offset for pagination (default 0). |
| organism | string | – | Filter by source organism scientific name (e.g., "Homo sapiens", "Escherichia coli"). |
| query | string | yes | Search query for protein name, PDB ID, keyword, or description (e.g., "kinase", "hemoglobin", "1ABC"). |
| Name | Type | Req | Description |
|---|---|---|---|
| hasMore | boolean | yes | Whether more results are available for pagination. |
| results | array | yes | Array of matching protein structures. |
| totalCount | integer | yes | Total number of matching structures. |
No examples provided.
protein_track_ligands Track Protein Ligands ~112
Find protein structures containing specific ligands, cofactors, drugs, or binding partners. Includes binding site details for drug discovery and molecular docking.
| Name | Type | Req | Description |
|---|---|---|---|
| filters | object | – | Additional filters for protein selection. |
| includeBindingSite | boolean | – | Include binding site residue details. |
| ligandQuery | object | yes | Ligand query: name (e.g., "ATP"), chemical ID, SMILES, or InChI. |
| limit | integer | – | Maximum number of results to return (1-100). |
| Name | Type | Req | Description |
|---|---|---|---|
| ligand | object | yes | Ligand identification and properties. |
| structures | array | yes | Protein structures containing the ligand. |
| totalCount | number | yes | Total number of structures containing the ligand. |
No examples provided.
How do I install the io.github.cyanheads/protein-mcp-server server?
io.github.cyanheads/protein-mcp-server runs locally as an npm package, launched with npx -y protein-mcp-server. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.
npm · protein-mcp-server
claude mcp add cyanheads-protein-mcp-server -- npx -y protein-mcp-server
What is the io.github.cyanheads/protein-mcp-server server?
io.github.cyanheads/protein-mcp-server is listed in the public MCP registry as io.github.cyanheads/protein-mcp-server. MCP Server for 3D protein structural data retrieval & analysis from RCSB PDB, PDBe, and UniProt. This page covers its npm package (protein-mcp-server).
Is the io.github.cyanheads/protein-mcp-server server safe to use?
io.github.cyanheads/protein-mcp-server scores 75 out of 100 on VerifyMCP. We recorded 10 known advisories against it as of 5 November 2026. It declares no install or post-install scripts. 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 io.github.cyanheads/protein-mcp-server server expose?
io.github.cyanheads/protein-mcp-server exposes 6 tools: protein_search_structures, protein_get_structure, protein_compare_structures, protein_find_similar, protein_track_ligands, protein_analyze_collection. Their descriptions and schemas cost roughly 827 tokens of context every time the server is loaded.
Is the io.github.cyanheads/protein-mcp-server server still maintained?
io.github.cyanheads/protein-mcp-server 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 io.github.cyanheads/protein-mcp-server server under?
io.github.cyanheads/protein-mcp-server declares the Apache-2.0 licence, which is OSI-approved. That covers the source only, and says nothing about the cost of any service it calls.