# io.github.cyanheads/protein-mcp-server

> MCP Server for 3D protein structural data retrieval & analysis from RCSB PDB, PDBe, and UniProt.

- name: io.github.cyanheads/protein-mcp-server
- version: 1.0.3
- connection class: L0 (run_local_package)
- trust: 70/100
- quality: –/100 (not scored)
- owner: not claimed
- descriptor: https://api.protogrid.dev/v1/servers/io.github.cyanheads%2Fprotein-mcp-server
- tools: https://api.protogrid.dev/v1/servers/io.github.cyanheads%2Fprotein-mcp-server/tools

**Runs on your machine: something must execute the package.** Only local packages are published (npm, PyPI, OCI, …). The registry never executes them, so tools are unknown until you run it.

## Connection (mcpServers)

```json
{
  "mcpServers": {
    "protein-mcp-server": {
      "command": "bun",
      "args": [
        "protein-mcp-server",
        "run",
        "start:stdio"
      ],
      "env": {
        "MCP_LOG_LEVEL": "info"
      }
    }
  }
}
```


## Trust

- hygiene: 100
- liveness: n/a
- freshness: 25
- provenance: 80
- drivers: +repository +namespace-matches-repo ~liveness-unmeasured -stale-383d
- Derived from observable signals (official registry feed and our own credential-free probes); no code audit performed.

## Quality –/100 (not scored)

Not scored: fewer than three checks apply, usually because no remote answered a credential-free probe or the server is a local package.

### protocol: n/a (weight 25)

- n/a `protocol.modern`, `protocol.stateless`, `protocol.transport`, `protocol.list_ttl`: no remote answered a protocol handshake (not probed yet, unreachable, or local-only)

### authorization: n/a (weight 15)

- n/a `auth.prm`, `auth.as_metadata`, `auth.cimd`: no remote uses OAuth
- n/a `auth.secret_in_url`: no templated URL

### tool hygiene: n/a (weight 30)

- n/a `tools.descriptions`, `tools.description_length`, `tools.schemas`, `tools.annotations`, `tools.directory_hints`, `tools.token_cost`, `tools.api_dump`: tool list unknown (behind auth, not probed, or empty)

### stability: n/a (weight 15)

- n/a `stability.changes`, `stability.rug_pull`: tool list unknown

### dependencies: 33 (weight 15)

- fail `deps.known_vulns`: 20 advisories to act on (malicious, or rated high or critical with a fix available): GHSA-8r9p-f939-6h3c in follow-redirects@1.16.0 (indirect, fixed in 1.16.1), GHSA-q3jh-wrc6-jgq8 in follow-redirects@1.16.0 (indirect, fixed in 1.16.1), GHSA-8r5x-fm3f-whwj in handlebars@4.7.9 (indirect, fixed in 4.7.10), ...; 34 more of lower severity or without a fix
- fail `deps.mcp_sdk_version`: @modelcontextprotocol/sdk 1.30.1 has 3 known advisories (GHSA-22jm-h49p-29qw, GHSA-6prh-2h8m-c8cw, GHSA-6qxp-vccf-f47h); update @modelcontextprotocol/sdk to 1.32.0 or later
- pass `deps.resolvable`: protein-mcp-server@1.0.3, protein-mcp-server@1.0.3 resolved: 914 packages

- tools: unknown
- badge: [![protogrid quality](https://protogrid.dev/badge/io.github.cyanheads/protein-mcp-server.svg)](https://protogrid.dev/servers/io.github.cyanheads/protein-mcp-server)
- Checks run on what our credential-free, read-only probes observe; tools are never called and no code audit is performed.

### Tool changes

_No tool definition changes recorded._

## Dependencies

- npm protein-mcp-server@1.0.3: resolved, 456 dependencies, MCP SDK @modelcontextprotocol/sdk 1.30.1
  - GHSA-8r5x-fm3f-whwj (critical) in `` handlebars@4.7.9 ``, indirect, fixed in `` 4.7.10 ``, advisory summary: "Handlebars: JavaScript Injection via AST Type Confusion in compile (bypass of CVE-2026-33937)" https://osv.dev/vulnerability/GHSA-8r5x-fm3f-whwj
  - GHSA-p8wg-vrv2-v86f (critical) in `` handlebars@4.7.9 ``, indirect, fixed in `` 4.7.10 ``, advisory summary: "Handlebars: JavaScript Injection via Own Property Check Bypass" https://osv.dev/vulnerability/GHSA-p8wg-vrv2-v86f
  - GHSA-22jm-h49p-29qw (high) in `` @modelcontextprotocol/sdk@1.30.1 ``, direct, fixed in `` 1.32.0 ``, advisory summary: "MCP TypeScript SDK: Experimental tasks were not tied to the session that created them" https://osv.dev/vulnerability/GHSA-22jm-h49p-29qw
  - GHSA-6qxp-vccf-f47h (high) in `` @modelcontextprotocol/sdk@1.30.1 ``, direct, fixed in `` 1.31.0 ``, advisory summary: "MCP TypeScript SDK: OAuth client could send credentials to an authorization server chosen by the MCP server" https://osv.dev/vulnerability/GHSA-6qxp-vccf-f47h
  - GHSA-q7rr-3cgh-j5r3 (high) in `` @opentelemetry/auto-instrumentations-node@0.64.6 ``, direct, fixed in `` 0.75.0 ``, advisory summary: "Prometheus exporter process crash via malformed HTTP request" https://osv.dev/vulnerability/GHSA-q7rr-3cgh-j5r3
  - GHSA-q7rr-3cgh-j5r3 (high) in `` @opentelemetry/exporter-prometheus@0.205.0 ``, indirect, fixed in `` 0.217.0 ``, advisory summary: "Prometheus exporter process crash via malformed HTTP request" https://osv.dev/vulnerability/GHSA-q7rr-3cgh-j5r3
  - GHSA-45rx-2jwx-cxfr (high) in `` @opentelemetry/propagator-jaeger@2.1.0 ``, indirect, fixed in `` 2.9.0 ``, advisory summary: "OpenTelemetry JavaScript: Denial of service in \`JaegerPropagator\` via unhandled exception on a malformed header" https://osv.dev/vulnerability/GHSA-45rx-2jwx-cxfr
  - GHSA-q7rr-3cgh-j5r3 (high) in `` @opentelemetry/sdk-node@0.205.0 ``, direct, fixed in `` 0.217.0 ``, advisory summary: "Prometheus exporter process crash via malformed HTTP request" https://osv.dev/vulnerability/GHSA-q7rr-3cgh-j5r3
  - GHSA-8r9p-f939-6h3c (high) in `` follow-redirects@1.16.0 ``, indirect, fixed in `` 1.16.1 ``, advisory summary: "follow-redirects sensitiveHeaders regex escaping can expose credential headers" https://osv.dev/vulnerability/GHSA-8r9p-f939-6h3c
  - GHSA-q3jh-wrc6-jgq8 (high) in `` follow-redirects@1.16.0 ``, indirect, fixed in `` 1.16.1 ``, advisory summary: "follow-redirects array-form headers bypass cross-origin credential stripping" https://osv.dev/vulnerability/GHSA-q3jh-wrc6-jgq8
  - GHSA-68fv-2mgg-jv7q (high) in `` source-map-js@1.2.1 ``, indirect, fixed in `` 1.2.2 ``, advisory summary: "source-map-js allows event-loop denial of service through indexed source-map section offsets" https://osv.dev/vulnerability/GHSA-68fv-2mgg-jv7q
  - GHSA-vghf-hv5q-vc2g (high) in `` validator@13.15.15 ``, direct, fixed in `` 13.15.22 ``, advisory summary: "Validator is Vulnerable to Incomplete Filtering of One or More Instances of Special Elements" https://osv.dev/vulnerability/GHSA-vghf-hv5q-vc2g
  - GHSA-vfj7-8cjw-p6xm (high) in `` braces@3.0.3 ``, indirect, no fix yet, advisory summary: "braces vulnerable to stack-exhaustion denial of service through deeply nested patterns" https://osv.dev/vulnerability/GHSA-vfj7-8cjw-p6xm
  - GHSA-6prh-2h8m-c8cw (moderate) in `` @modelcontextprotocol/sdk@1.30.1 ``, direct, fixed in `` 1.32.0 ``, advisory summary: "MCP TypeScript client SDK: HTTP client transports and OAuth requests followed cross-origin redirects and re-sent custom headers and request bodies" https://osv.dev/vulnerability/GHSA-6prh-2h8m-c8cw
  - GHSA-8988-4f7v-96qf (moderate) in `` @opentelemetry/core@2.1.0 ``, indirect, fixed in `` 2.8.0 ``, advisory summary: "OpenTelemetry Core: Unbounded memory allocation in W3C Baggage propagation" https://osv.dev/vulnerability/GHSA-8988-4f7v-96qf
  - GHSA-qqmp-wf37-98f9 (moderate) in `` @opentelemetry/instrumentation-cassandra-driver@0.51.3 ``, indirect, fixed in `` 0.66.0 ``, advisory summary: "Multiple @opentelemetry/instrumentation-\* packages expose database username via unconditional db.user span attribute" https://osv.dev/vulnerability/GHSA-qqmp-wf37-98f9
  - GHSA-qqmp-wf37-98f9 (moderate) in `` @opentelemetry/instrumentation-knex@0.50.2 ``, indirect, fixed in `` 0.65.0 ``, advisory summary: "Multiple @opentelemetry/instrumentation-\* packages expose database username via unconditional db.user span attribute" https://osv.dev/vulnerability/GHSA-qqmp-wf37-98f9
  - GHSA-qqmp-wf37-98f9 (moderate) in `` @opentelemetry/instrumentation-mongoose@0.52.3 ``, indirect, fixed in `` 0.67.0 ``, advisory summary: "Multiple @opentelemetry/instrumentation-\* packages expose database username via unconditional db.user span attribute" https://osv.dev/vulnerability/GHSA-qqmp-wf37-98f9
  - GHSA-qqmp-wf37-98f9 (moderate) in `` @opentelemetry/instrumentation-mysql@0.51.3 ``, indirect, fixed in `` 0.67.0 ``, advisory summary: "Multiple @opentelemetry/instrumentation-\* packages expose database username via unconditional db.user span attribute" https://osv.dev/vulnerability/GHSA-qqmp-wf37-98f9
  - GHSA-qqmp-wf37-98f9 (moderate) in `` @opentelemetry/instrumentation-mysql2@0.52.3 ``, indirect, fixed in `` 0.67.0 ``, advisory summary: "Multiple @opentelemetry/instrumentation-\* packages expose database username via unconditional db.user span attribute" https://osv.dev/vulnerability/GHSA-qqmp-wf37-98f9
  - GHSA-qqmp-wf37-98f9 (moderate) in `` @opentelemetry/instrumentation-oracledb@0.31.3 ``, indirect, fixed in `` 0.46.0 ``, advisory summary: "Multiple @opentelemetry/instrumentation-\* packages expose database username via unconditional db.user span attribute" https://osv.dev/vulnerability/GHSA-qqmp-wf37-98f9
  - GHSA-qqmp-wf37-98f9 (moderate) in `` @opentelemetry/instrumentation-pg@0.58.3 ``, indirect, fixed in `` 0.73.0 ``, advisory summary: "Multiple @opentelemetry/instrumentation-\* packages expose database username via unconditional db.user span attribute" https://osv.dev/vulnerability/GHSA-qqmp-wf37-98f9
  - GHSA-qqmp-wf37-98f9 (moderate) in `` @opentelemetry/instrumentation-tedious@0.24.3 ``, indirect, fixed in `` 0.40.0 ``, advisory summary: "Multiple @opentelemetry/instrumentation-\* packages expose database username via unconditional db.user span attribute" https://osv.dev/vulnerability/GHSA-qqmp-wf37-98f9
  - GHSA-xw65-4hp5-5hc7 (moderate) in `` handlebars@4.7.9 ``, indirect, fixed in `` 4.7.10 ``, advisory summary: "Handlebars: JavaScript Injection via Unsafe Inline Embedding of Precompiled Templates" https://osv.dev/vulnerability/GHSA-xw65-4hp5-5hc7
  - GHSA-5r4p-p66f-jhc7 (moderate) in `` hono@4.13.9 ``, direct, fixed in `` 4.13.11 ``, advisory summary: "Hono: \`serveStatic\` decodes the request path a second time, leading to bypass of middleware on static paths" https://osv.dev/vulnerability/GHSA-5r4p-p66f-jhc7
  - GHSA-cv27-6wvh-8x7j (moderate) in `` sanitize-html@2.17.7 ``, direct, fixed in `` 2.18.0 ``, advisory summary: "ApostropheCMS: Incomplete CVE-2026-53606: \`meta http-equiv=refresh\` \`content\` still ships \`javascript:\` / \`data:\` URLs" https://osv.dev/vulnerability/GHSA-cv27-6wvh-8x7j
  - GHSA-x3q4-9hxx-gx8m (moderate) in `` sanitize-html@2.17.7 ``, direct, fixed in `` 2.18.0 ``, advisory summary: "ApostropheCMS sanitize-html: nonTextTags discard region ends early on an implied close, letting \<noscript\> content render" https://osv.dev/vulnerability/GHSA-x3q4-9hxx-gx8m
  - GHSA-w5hq-g745-h8pq (moderate) in `` uuid@9.0.1 ``, indirect, fixed in `` 11.1.1 ``, advisory summary: "uuid: Missing buffer bounds check in v3/v5/v6 when buf is provided" https://osv.dev/vulnerability/GHSA-w5hq-g745-h8pq
  - GHSA-9965-vmph-33xx (moderate) in `` validator@13.15.15 ``, direct, fixed in `` 13.15.20 ``, advisory summary: "validator.js has a URL validation bypass vulnerability in its isURL function" https://osv.dev/vulnerability/GHSA-9965-vmph-33xx
  - GHSA-374f-7chj-9948 (low) in `` sanitize-html@2.17.7 ``, direct, fixed in `` 2.18.0 ``, advisory summary: "ApostropheCMS sanitize-html: SMIL animation namespace-prefix bypass allows javascript: URI injection (XSS)" https://osv.dev/vulnerability/GHSA-374f-7chj-9948
- npm protein-mcp-server@1.0.3: resolved, 456 dependencies, MCP SDK @modelcontextprotocol/sdk 1.30.1
  - GHSA-8r5x-fm3f-whwj (critical) in `` handlebars@4.7.9 ``, indirect, fixed in `` 4.7.10 ``, advisory summary: "Handlebars: JavaScript Injection via AST Type Confusion in compile (bypass of CVE-2026-33937)" https://osv.dev/vulnerability/GHSA-8r5x-fm3f-whwj
  - GHSA-p8wg-vrv2-v86f (critical) in `` handlebars@4.7.9 ``, indirect, fixed in `` 4.7.10 ``, advisory summary: "Handlebars: JavaScript Injection via Own Property Check Bypass" https://osv.dev/vulnerability/GHSA-p8wg-vrv2-v86f
  - GHSA-22jm-h49p-29qw (high) in `` @modelcontextprotocol/sdk@1.30.1 ``, direct, fixed in `` 1.32.0 ``, advisory summary: "MCP TypeScript SDK: Experimental tasks were not tied to the session that created them" https://osv.dev/vulnerability/GHSA-22jm-h49p-29qw
  - GHSA-6qxp-vccf-f47h (high) in `` @modelcontextprotocol/sdk@1.30.1 ``, direct, fixed in `` 1.31.0 ``, advisory summary: "MCP TypeScript SDK: OAuth client could send credentials to an authorization server chosen by the MCP server" https://osv.dev/vulnerability/GHSA-6qxp-vccf-f47h
  - GHSA-q7rr-3cgh-j5r3 (high) in `` @opentelemetry/auto-instrumentations-node@0.64.6 ``, direct, fixed in `` 0.75.0 ``, advisory summary: "Prometheus exporter process crash via malformed HTTP request" https://osv.dev/vulnerability/GHSA-q7rr-3cgh-j5r3
  - GHSA-q7rr-3cgh-j5r3 (high) in `` @opentelemetry/exporter-prometheus@0.205.0 ``, indirect, fixed in `` 0.217.0 ``, advisory summary: "Prometheus exporter process crash via malformed HTTP request" https://osv.dev/vulnerability/GHSA-q7rr-3cgh-j5r3
  - GHSA-45rx-2jwx-cxfr (high) in `` @opentelemetry/propagator-jaeger@2.1.0 ``, indirect, fixed in `` 2.9.0 ``, advisory summary: "OpenTelemetry JavaScript: Denial of service in \`JaegerPropagator\` via unhandled exception on a malformed header" https://osv.dev/vulnerability/GHSA-45rx-2jwx-cxfr
  - GHSA-q7rr-3cgh-j5r3 (high) in `` @opentelemetry/sdk-node@0.205.0 ``, direct, fixed in `` 0.217.0 ``, advisory summary: "Prometheus exporter process crash via malformed HTTP request" https://osv.dev/vulnerability/GHSA-q7rr-3cgh-j5r3
  - GHSA-8r9p-f939-6h3c (high) in `` follow-redirects@1.16.0 ``, indirect, fixed in `` 1.16.1 ``, advisory summary: "follow-redirects sensitiveHeaders regex escaping can expose credential headers" https://osv.dev/vulnerability/GHSA-8r9p-f939-6h3c
  - GHSA-q3jh-wrc6-jgq8 (high) in `` follow-redirects@1.16.0 ``, indirect, fixed in `` 1.16.1 ``, advisory summary: "follow-redirects array-form headers bypass cross-origin credential stripping" https://osv.dev/vulnerability/GHSA-q3jh-wrc6-jgq8
  - GHSA-68fv-2mgg-jv7q (high) in `` source-map-js@1.2.1 ``, indirect, fixed in `` 1.2.2 ``, advisory summary: "source-map-js allows event-loop denial of service through indexed source-map section offsets" https://osv.dev/vulnerability/GHSA-68fv-2mgg-jv7q
  - GHSA-vghf-hv5q-vc2g (high) in `` validator@13.15.15 ``, direct, fixed in `` 13.15.22 ``, advisory summary: "Validator is Vulnerable to Incomplete Filtering of One or More Instances of Special Elements" https://osv.dev/vulnerability/GHSA-vghf-hv5q-vc2g
  - GHSA-vfj7-8cjw-p6xm (high) in `` braces@3.0.3 ``, indirect, no fix yet, advisory summary: "braces vulnerable to stack-exhaustion denial of service through deeply nested patterns" https://osv.dev/vulnerability/GHSA-vfj7-8cjw-p6xm
  - GHSA-6prh-2h8m-c8cw (moderate) in `` @modelcontextprotocol/sdk@1.30.1 ``, direct, fixed in `` 1.32.0 ``, advisory summary: "MCP TypeScript client SDK: HTTP client transports and OAuth requests followed cross-origin redirects and re-sent custom headers and request bodies" https://osv.dev/vulnerability/GHSA-6prh-2h8m-c8cw
  - GHSA-8988-4f7v-96qf (moderate) in `` @opentelemetry/core@2.1.0 ``, indirect, fixed in `` 2.8.0 ``, advisory summary: "OpenTelemetry Core: Unbounded memory allocation in W3C Baggage propagation" https://osv.dev/vulnerability/GHSA-8988-4f7v-96qf
  - GHSA-qqmp-wf37-98f9 (moderate) in `` @opentelemetry/instrumentation-cassandra-driver@0.51.3 ``, indirect, fixed in `` 0.66.0 ``, advisory summary: "Multiple @opentelemetry/instrumentation-\* packages expose database username via unconditional db.user span attribute" https://osv.dev/vulnerability/GHSA-qqmp-wf37-98f9
  - GHSA-qqmp-wf37-98f9 (moderate) in `` @opentelemetry/instrumentation-knex@0.50.2 ``, indirect, fixed in `` 0.65.0 ``, advisory summary: "Multiple @opentelemetry/instrumentation-\* packages expose database username via unconditional db.user span attribute" https://osv.dev/vulnerability/GHSA-qqmp-wf37-98f9
  - GHSA-qqmp-wf37-98f9 (moderate) in `` @opentelemetry/instrumentation-mongoose@0.52.3 ``, indirect, fixed in `` 0.67.0 ``, advisory summary: "Multiple @opentelemetry/instrumentation-\* packages expose database username via unconditional db.user span attribute" https://osv.dev/vulnerability/GHSA-qqmp-wf37-98f9
  - GHSA-qqmp-wf37-98f9 (moderate) in `` @opentelemetry/instrumentation-mysql@0.51.3 ``, indirect, fixed in `` 0.67.0 ``, advisory summary: "Multiple @opentelemetry/instrumentation-\* packages expose database username via unconditional db.user span attribute" https://osv.dev/vulnerability/GHSA-qqmp-wf37-98f9
  - GHSA-qqmp-wf37-98f9 (moderate) in `` @opentelemetry/instrumentation-mysql2@0.52.3 ``, indirect, fixed in `` 0.67.0 ``, advisory summary: "Multiple @opentelemetry/instrumentation-\* packages expose database username via unconditional db.user span attribute" https://osv.dev/vulnerability/GHSA-qqmp-wf37-98f9
  - GHSA-qqmp-wf37-98f9 (moderate) in `` @opentelemetry/instrumentation-oracledb@0.31.3 ``, indirect, fixed in `` 0.46.0 ``, advisory summary: "Multiple @opentelemetry/instrumentation-\* packages expose database username via unconditional db.user span attribute" https://osv.dev/vulnerability/GHSA-qqmp-wf37-98f9
  - GHSA-qqmp-wf37-98f9 (moderate) in `` @opentelemetry/instrumentation-pg@0.58.3 ``, indirect, fixed in `` 0.73.0 ``, advisory summary: "Multiple @opentelemetry/instrumentation-\* packages expose database username via unconditional db.user span attribute" https://osv.dev/vulnerability/GHSA-qqmp-wf37-98f9
  - GHSA-qqmp-wf37-98f9 (moderate) in `` @opentelemetry/instrumentation-tedious@0.24.3 ``, indirect, fixed in `` 0.40.0 ``, advisory summary: "Multiple @opentelemetry/instrumentation-\* packages expose database username via unconditional db.user span attribute" https://osv.dev/vulnerability/GHSA-qqmp-wf37-98f9
  - GHSA-xw65-4hp5-5hc7 (moderate) in `` handlebars@4.7.9 ``, indirect, fixed in `` 4.7.10 ``, advisory summary: "Handlebars: JavaScript Injection via Unsafe Inline Embedding of Precompiled Templates" https://osv.dev/vulnerability/GHSA-xw65-4hp5-5hc7
  - GHSA-5r4p-p66f-jhc7 (moderate) in `` hono@4.13.9 ``, direct, fixed in `` 4.13.11 ``, advisory summary: "Hono: \`serveStatic\` decodes the request path a second time, leading to bypass of middleware on static paths" https://osv.dev/vulnerability/GHSA-5r4p-p66f-jhc7
  - GHSA-cv27-6wvh-8x7j (moderate) in `` sanitize-html@2.17.7 ``, direct, fixed in `` 2.18.0 ``, advisory summary: "ApostropheCMS: Incomplete CVE-2026-53606: \`meta http-equiv=refresh\` \`content\` still ships \`javascript:\` / \`data:\` URLs" https://osv.dev/vulnerability/GHSA-cv27-6wvh-8x7j
  - GHSA-x3q4-9hxx-gx8m (moderate) in `` sanitize-html@2.17.7 ``, direct, fixed in `` 2.18.0 ``, advisory summary: "ApostropheCMS sanitize-html: nonTextTags discard region ends early on an implied close, letting \<noscript\> content render" https://osv.dev/vulnerability/GHSA-x3q4-9hxx-gx8m
  - GHSA-w5hq-g745-h8pq (moderate) in `` uuid@9.0.1 ``, indirect, fixed in `` 11.1.1 ``, advisory summary: "uuid: Missing buffer bounds check in v3/v5/v6 when buf is provided" https://osv.dev/vulnerability/GHSA-w5hq-g745-h8pq
  - GHSA-9965-vmph-33xx (moderate) in `` validator@13.15.15 ``, direct, fixed in `` 13.15.20 ``, advisory summary: "validator.js has a URL validation bypass vulnerability in its isURL function" https://osv.dev/vulnerability/GHSA-9965-vmph-33xx
  - GHSA-374f-7chj-9948 (low) in `` sanitize-html@2.17.7 ``, direct, fixed in `` 2.18.0 ``, advisory summary: "ApostropheCMS sanitize-html: SMIL animation namespace-prefix bypass allows javascript: URI injection (XSS)" https://osv.dev/vulnerability/GHSA-374f-7chj-9948

Dependency graphs from deps.dev; advisories from OSV.dev, including the GitHub Advisory Database and the PyPI Advisory Database; all CC BY 4.0.

## Remotes

_none_

## Packages

- npm protein-mcp-server@1.0.3
- npm protein-mcp-server@1.0.3

## Tools (0)

_none observed_