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8 clients · secrets stay placeholders

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

claude mcp add protein-mcp-server -e "MCP_LOG_LEVEL=info" -- bun protein-mcp-server run start:stdio

[mcp_servers.protein-mcp-server]
command = "bun"
args = ["protein-mcp-server", "run", "start:stdio"]
env = { "MCP_LOG_LEVEL" = "info" }

{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "protein-mcp-server": {
      "type": "local",
      "command": [
        "bun",
        "protein-mcp-server",
        "run",
        "start:stdio"
      ],
      "enabled": true,
      "environment": {
        "MCP_LOG_LEVEL": "info"
      }
    }
  }
}

{
  "mcpServers": {
    "protein-mcp-server": {
      "command": "bun",
      "args": [
        "protein-mcp-server",
        "run",
        "start:stdio"
      ],
      "env": {
        "MCP_LOG_LEVEL": "info"
      }
    }
  },
  "deeplink": "cursor://anysphere.cursor-deeplink/mcp/install?name=protein-mcp-server&config=eyJjb21tYW5kIjoiYnVuIiwiYXJncyI6WyJwcm90ZWluLW1jcC1zZXJ2ZXIiLCJydW4iLCJzdGFydDpzdGRpbyJdLCJlbnYiOnsiTUNQX0xPR19MRVZFTCI6ImluZm8ifX0%3D"
}

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

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

extensions:
  "protein-mcp-server":
    enabled: true
    name: "protein-mcp-server"
    type: stdio
    cmd: "bun"
    args:
      - "protein-mcp-server"
      - "run"
      - "start:stdio"
    envs:
      "MCP_LOG_LEVEL": "info"
    timeout: 300

This is a local package: the command runs on your machine.

Quality – / 100not scored

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

protocoln/a · weight 25

n/a
protocol.modern, protocol.stateless, protocol.transport, protocol.list_ttlno remote answered a protocol handshake (not probed yet, unreachable, or local-only)

authorizationn/a · weight 15

n/a
auth.prm, auth.as_metadata, auth.cimdno remote uses OAuth
n/a
auth.secret_in_urlno templated URL

tool hygienen/a · weight 30

n/a
tools.descriptions, tools.description_length, tools.schemas, tools.annotations, tools.directory_hints, tools.token_cost, tools.api_dumptool list unknown (behind auth, not probed, or empty)

stabilityn/a · weight 15

n/a
stability.changes, stability.rug_pulltool list unknown

dependencies33 · weight 15

fail
deps.known_vulns16 advisories to act on (malicious, or rated high or critical with a fix available): GHSA-8r5x-fm3f-whwj in [email protected] (indirect, fixed in 4.7.10), GHSA-p8wg-vrv2-v86f in [email protected] (indirect, fixed in 4.7.10), GHSA-q7rr-3cgh-j5r3 in @opentelemetry/[email protected] (direct, fixed in 0.75.0), ...; 26 more of lower severity or without a fix
fail
deps.mcp_sdk_version@modelcontextprotocol/sdk 1.30.1 has 1 known advisory (GHSA-6qxp-vccf-f47h); update @modelcontextprotocol/sdk to 1.31.0 or later
pass
deps.resolvable[email protected], [email protected] resolved: 914 packages

Tool list unknown · checked 2026-10-20 11:40 UTC

Tool changes

No tool definition changes recorded. A server's first observation is its baseline; later probes record what changes.

Checks run on what our credential-free, read-only probes observe; tools are never called and no code audit is performed. How it is computed.

Trust 70 / 100

provenance80

livenessn/a

freshness25

hygiene100

+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. How it is computed.

Dependencies

[email protected] npm456 dependencies, resolved · MCP SDK @modelcontextprotocol/sdk 1.30.1 · advisories checked 2026-10-19

advisory	severity	package	fixed in
GHSA-8r5x-fm3f-whwjHandlebars: JavaScript Injection via AST Type Confusion in compile (bypass of CVE-2026-33937)	critical	`[email protected]`indirect	fixed in `4.7.10`
GHSA-p8wg-vrv2-v86fHandlebars: JavaScript Injection via Own Property Check Bypass	critical	`[email protected]`indirect	fixed in `4.7.10`
GHSA-6qxp-vccf-f47hMCP TypeScript SDK: OAuth client could send credentials to an authorization server chosen by the MCP server	high	`@modelcontextprotocol/[email protected]`MCP SDK, direct	fixed in `1.31.0`
GHSA-q7rr-3cgh-j5r3Prometheus exporter process crash via malformed HTTP request	high	`@opentelemetry/[email protected]`direct	fixed in `0.75.0`
GHSA-q7rr-3cgh-j5r3Prometheus exporter process crash via malformed HTTP request	high	`@opentelemetry/[email protected]`indirect	fixed in `0.217.0`
GHSA-45rx-2jwx-cxfrOpenTelemetry JavaScript: Denial of service in `JaegerPropagator` via unhandled exception on a malformed header	high	`@opentelemetry/[email protected]`indirect	fixed in `2.9.0`
GHSA-q7rr-3cgh-j5r3Prometheus exporter process crash via malformed HTTP request	high	`@opentelemetry/[email protected]`direct	fixed in `0.217.0`
GHSA-68fv-2mgg-jv7qsource-map-js allows event-loop denial of service through indexed source-map section offsets	high	`[email protected]`indirect	fixed in `1.2.2`
GHSA-vghf-hv5q-vc2gValidator is Vulnerable to Incomplete Filtering of One or More Instances of Special Elements	high	`[email protected]`direct	fixed in `13.15.22`
GHSA-vfj7-8cjw-p6xmbraces vulnerable to stack-exhaustion denial of service through deeply nested patterns	high	`[email protected]`indirect	no fix yet

12 more advisories in the dependencies endpoint.

[email protected] npm456 dependencies, resolved · MCP SDK @modelcontextprotocol/sdk 1.30.1 · advisories checked 2026-10-19

advisory	severity	package	fixed in
GHSA-8r5x-fm3f-whwjHandlebars: JavaScript Injection via AST Type Confusion in compile (bypass of CVE-2026-33937)	critical	`[email protected]`indirect	fixed in `4.7.10`
GHSA-p8wg-vrv2-v86fHandlebars: JavaScript Injection via Own Property Check Bypass	critical	`[email protected]`indirect	fixed in `4.7.10`
GHSA-6qxp-vccf-f47hMCP TypeScript SDK: OAuth client could send credentials to an authorization server chosen by the MCP server	high	`@modelcontextprotocol/[email protected]`MCP SDK, direct	fixed in `1.31.0`
GHSA-q7rr-3cgh-j5r3Prometheus exporter process crash via malformed HTTP request	high	`@opentelemetry/[email protected]`direct	fixed in `0.75.0`
GHSA-q7rr-3cgh-j5r3Prometheus exporter process crash via malformed HTTP request	high	`@opentelemetry/[email protected]`indirect	fixed in `0.217.0`
GHSA-45rx-2jwx-cxfrOpenTelemetry JavaScript: Denial of service in `JaegerPropagator` via unhandled exception on a malformed header	high	`@opentelemetry/[email protected]`indirect	fixed in `2.9.0`
GHSA-q7rr-3cgh-j5r3Prometheus exporter process crash via malformed HTTP request	high	`@opentelemetry/[email protected]`direct	fixed in `0.217.0`
GHSA-68fv-2mgg-jv7qsource-map-js allows event-loop denial of service through indexed source-map section offsets	high	`[email protected]`indirect	fixed in `1.2.2`
GHSA-vghf-hv5q-vc2gValidator is Vulnerable to Incomplete Filtering of One or More Instances of Special Elements	high	`[email protected]`direct	fixed in `13.15.22`
GHSA-vfj7-8cjw-p6xmbraces vulnerable to stack-exhaustion denial of service through deeply nested patterns	high	`[email protected]`indirect	no fix yet

12 more advisories in the dependencies endpoint.

Dependency graphs from deps.dev; advisories from OSV.dev, including the GitHub Advisory Database and the PyPI Advisory Database; all CC BY 4.0. The graph is what a clean install of this version resolves today; nothing was installed or run. How it is checked.

Endpoints

package	registry	version	runtime	secrets
`protein-mcp-server`	npm	1.0.3	bun
`protein-mcp-server`	npm	1.0.3	bun

Tools (0)

No tools observed. Local packages are never executed by the registry.

Schemas: list_tools.

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Official server.json

{
  "name": "io.github.cyanheads/protein-mcp-server",
  "$schema": "https://static.modelcontextprotocol.io/schemas/2025-09-29/server.schema.json",
  "version": "1.0.3",
  "packages": [
    {
      "version": "1.0.3",
      "transport": {
        "type": "stdio"
      },
      "identifier": "protein-mcp-server",
      "runtimeHint": "bun",
      "registryType": "npm",
      "registryBaseUrl": "https://registry.npmjs.org",
      "packageArguments": [
        {
          "type": "positional",
          "value": "run"
        },
        {
          "type": "positional",
          "value": "start:stdio"
        }
      ],
      "environmentVariables": [
        {
          "name": "MCP_LOG_LEVEL",
          "format": "string",
          "default": "info",
          "description": "Sets the minimum log level for output (e.g., 'debug', 'info', 'warn')."
        }
      ]
    },
    {
      "version": "1.0.3",
      "transport": {
        "url": "http://localhost:3010/mcp",
        "type": "streamable-http"
      },
      "identifier": "protein-mcp-server",
      "runtimeHint": "bun",
      "registryType": "npm",
      "registryBaseUrl": "https://registry.npmjs.org",
      "packageArguments": [
        {
          "type": "positional",
          "value": "run"
        },
        {
          "type": "positional",
          "value": "start:http"
        }
      ],
      "environmentVariables": [
        {
          "name": "MCP_HTTP_HOST",
          "format": "string",
          "default": "127.0.0.1",
          "description": "The hostname for the HTTP server."
        },
        {
          "name": "MCP_HTTP_PORT",
          "format": "string",
          "default": "3010",
          "description": "The port to run the HTTP server on."
        },
        {
          "name": "MCP_HTTP_ENDPOINT_PATH",
          "format": "string",
          "default": "/mcp",
          "description": "The endpoint path for the MCP server."
        },
        {
          "name": "MCP_AUTH_MODE",
          "format": "string",
          "default": "none",
          "description": "Authentication mode to use: 'none', 'jwt', or 'oauth'."
        },
        {
          "name": "MCP_LOG_LEVEL",
          "format": "string",
          "default": "info",
          "description": "Sets the minimum log level for output (e.g., 'debug', 'info', 'warn')."
        }
      ]
    }
  ],
  "repository": {
    "url": "https://github.com/cyanheads/protein-mcp-server",
    "source": "github"
  },
  "description": "MCP Server for 3D protein structural data retrieval & analysis from RCSB PDB, PDBe, and UniProt."
}