Skills/PyPI/pdbe-mcp-server

pdbe-mcp-server@2.0.1

VERIFIED· not started

Publisher claims: "A Model Context Protocol (MCP) server for accessing PDBe (Protein Data Bank in Europe) structural biology data and services" Observed in sandbox: no network, touches nothing outside the project, writes no memory.

Registry PyPI (MCP server)Publisher sreenath-sasidharan-nair-sreenath · publishing for 378 daysInstalls 920Last detonated 30 min ago
$claude mcp add pdbe-mcp-server -- uvx pdbe-mcp-server
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Coverage

Not started: dependency install failed; the server itself was not observed.
Tested
the dependency install step · every file read, file written and host contacted by what ran
Not tested
server startup · the tool list · tool behavior

What this means for the label: Verified here covers what ran. The server's tools were not exercised with a real credential, so nothing about their behavior is asserted; the credential summary below says what to do with that.

Before you give it your token

It will ask for
NEO4J_PASSWORDConfiguration, not credentials: ALL_SERVERS, CORS_ORIGINS, JSON_RESPONSE, MAX_CONCURRENT_MCP_REQUESTS, NEO4J_DATABASE, NEO4J_URI, NEO4J_USERNAME, ROOT_PREFIX, SHUTDOWN_DRAIN_TIMEOUT_SECONDS, TOOL_TIMEOUT_SECONDS, TOON_ENABLED
Where it talks to
no vendor host named in the codeAlso ebi.ac.uk, wwpdb.org — not the publisher's domain; check what for before connecting.
What the honeypot saw
no credential files read · no network
What we could not test
server startup · the tool list · tool behavior

Connect it with a scoped credential, under the guard, and read the third-party hosts first. The code names ebi.ac.uk, wwpdb.org as well as its own vendor. The guard injects NEO4J_PASSWORD only into requests to the host you bind (and its subdomains) and refuses the rest.

$vet-skills run --net declared -- uvx pdbe-mcp-server

Never paste a credential into a chat, a ticket or a report, including ours. How the guard holds it.

Is [email protected] safe to install?

KillerSkills ran it in the KillerSkills honeypot sandbox (2 scenarios; not started: dependency install failed; the server itself was not observed) on 2026-11-14 and scored it 87/100 (Verified). In what ran, nothing we could detect went wrong: no undeclared network egress, no credential reads, no persistent instruction writes. What it does with a real credential was not observed; the static findings and the publisher carry the rest of the score. Summary: no network, touches nothing outside the project, writes no memory.

Behavior trace

Honeypot run · 0 s · 2 scenarios · 0 deviations
t+CategoryObserved action
0.0sprocessno install scripts in bundle
0.1sprocessdependency install exit 1 ·
0.1sclaimednot started: dependency install failed (exit 1); the server itself was not observed
0.1sprocessscript backend runs setup only
0.2sprocessno install scripts to re-run

Static findings

MEDIUM
MCP server using network transport (SSE/HTTP)pdbe_mcp_server/graph_tools.py:11 · MCP server using network transport (SSE/HTTP) — data sent over networkfrom pdbe_mcp_server.utils import HTMLStripper, HTTPClientFix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
Process kill commandpdbe_mcp_server/execution.py:80 · Process kill command — agent can terminate processesCancellation cannot kill a Python thread. Shield the worker task so AnyIO'sFix: Build commands from fixed arguments; do not interpolate untrusted strings into a shell.
AST05
MEDIUM
MCP server using network transport (SSE/HTTP)pdbe_mcp_server/comparison_tools.py:9 · MCP server using network transport (SSE/HTTP) — data sent over networkfrom pdbe_mcp_server.utils import HTTPClientFix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
MCP server using network transport (SSE/HTTP)pdbe_mcp_server/api_tools.py:16 · MCP server using network transport (SSE/HTTP) — data sent over networkfrom pdbe_mcp_server.utils import HTTPClientFix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
MCP server using network transport (SSE/HTTP)pdbe_mcp_server/ai_summary_tools.py:9 · MCP server using network transport (SSE/HTTP) — data sent over networkfrom pdbe_mcp_server.utils import HTTPClientFix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
MCP server using network transport (SSE/HTTP)tests/test_ai_summary_tools.py:100 · MCP server using network transport (SSE/HTTP) — data sent over networkmonkeypatch.setattr("pdbe_mcp_server.ai_summary_tools.HTTPClient.get", get)Fix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
Python subprocess execution detectedtests/test_remote_lifespan.py:53 · Python subprocess execution detectedresult = subprocess.run(Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
MEDIUM
MCP server using network transport (SSE/HTTP)tests/test_http_deadlines.py:11 · MCP server using network transport (SSE/HTTP) — data sent over networkfrom pdbe_mcp_server.utils import HTTPClientFix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
MCP server using network transport (SSE/HTTP)tests/test_utils.py:8 · MCP server using network transport (SSE/HTTP) — data sent over networkfrom pdbe_mcp_server.utils import HTMLStripper, HTTPClientFix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
MCP server using network transport (SSE/HTTP)tests/test_api_tools.py:46 · MCP server using network transport (SSE/HTTP) — data sent over network@patch("pdbe_mcp_server.api_tools.HTTPClient.get")Fix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
MCP server using network transport (SSE/HTTP)tests/test_graph_tools.py:34 · MCP server using network transport (SSE/HTTP) — data sent over network@patch("pdbe_mcp_server.graph_tools.HTTPClient.get")Fix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
MCP server using network transport (SSE/HTTP)tests/test_api_tools.py:32 · MCP server using network transport (SSE/HTTP) — data sent over network@patch("pdbe_mcp_server.api_tools.HTTPClient.get")Fix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
MCP server using network transport (SSE/HTTP)pdbe_mcp_server/search_tools.py:11 · MCP server using network transport (SSE/HTTP) — data sent over networkfrom pdbe_mcp_server.utils import HTTPClientFix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
MCP server using network transport (SSE/HTTP)tests/test_api_tools.py:129 · MCP server using network transport (SSE/HTTP) — data sent over network@patch("pdbe_mcp_server.api_tools.HTTPClient.get")Fix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
MCP server using network transport (SSE/HTTP)tests/test_search_tools.py:72 · MCP server using network transport (SSE/HTTP) — data sent over network@patch("pdbe_mcp_server.search_tools.HTTPClient.get")Fix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
MCP server using network transport (SSE/HTTP)tests/test_api_tools.py:91 · MCP server using network transport (SSE/HTTP) — data sent over network@patch("pdbe_mcp_server.api_tools.HTTPClient.get")Fix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
MCP server using network transport (SSE/HTTP)pdbe_mcp_server/remote_server.py:32 · MCP server using network transport (SSE/HTTP) — data sent over networkfrom pdbe_mcp_server.utils import HTTPClientFix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
MCP server using network transport (SSE/HTTP)tests/test_search_tools.py:139 · MCP server using network transport (SSE/HTTP) — data sent over network@patch("pdbe_mcp_server.search_tools.HTTPClient.get")Fix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
MCP server using network transport (SSE/HTTP)tests/test_graph_tools.py:19 · MCP server using network transport (SSE/HTTP) — data sent over network@patch("pdbe_mcp_server.graph_tools.HTTPClient.get")Fix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
MCP server using network transport (SSE/HTTP)tests/test_graph_tools.py:48 · MCP server using network transport (SSE/HTTP) — data sent over network@patch("pdbe_mcp_server.graph_tools.HTTPClient.get")Fix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
MCP server using network transport (SSE/HTTP)tests/test_search_tools.py:95 · MCP server using network transport (SSE/HTTP) — data sent over network@patch("pdbe_mcp_server.search_tools.HTTPClient.get")Fix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
MCP server using network transport (SSE/HTTP)tests/test_tool_names.py:100 · MCP server using network transport (SSE/HTTP) — data sent over network"pdbe_mcp_server.ai_summary_tools.HTTPClient.get",Fix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
MCP server using network transport (SSE/HTTP)tests/test_search_tools.py:49 · MCP server using network transport (SSE/HTTP) — data sent over network@patch("pdbe_mcp_server.search_tools.HTTPClient.get")Fix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
MCP server using network transport (SSE/HTTP)tests/test_graph_tools.py:62 · MCP server using network transport (SSE/HTTP) — data sent over network@patch("pdbe_mcp_server.graph_tools.HTTPClient.get")Fix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
MCP server using network transport (SSE/HTTP)tests/test_graph_tools.py:77 · MCP server using network transport (SSE/HTTP) — data sent over network@patch("pdbe_mcp_server.graph_tools.HTTPClient.get")Fix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
MCP server using network transport (SSE/HTTP)tests/test_api_tools.py:114 · MCP server using network transport (SSE/HTTP) — data sent over network@patch("pdbe_mcp_server.api_tools.HTTPClient.get")Fix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
MCP server using network transport (SSE/HTTP)tests/test_ai_summary_tools.py:116 · MCP server using network transport (SSE/HTTP) — data sent over networkmonkeypatch.setattr("pdbe_mcp_server.ai_summary_tools.HTTPClient.get", get)Fix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
MCP server using network transport (SSE/HTTP)tests/test_search_tools.py:120 · MCP server using network transport (SSE/HTTP) — data sent over network@patch("pdbe_mcp_server.search_tools.HTTPClient.get")Fix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
MCP server using network transport (SSE/HTTP)tests/test_remote_lifespan.py:47 · MCP server using network transport (SSE/HTTP) — data sent over networkfrom pdbe_mcp_server.utils import HTTPClientFix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04
MEDIUM
MCP server using network transport (SSE/HTTP)pdbe_mcp_server/remote_server.py:31 · MCP server using network transport (SSE/HTTP) — data sent over networkfrom pdbe_mcp_server.skills import skill_http_requestFix: Namespace tool names and keep tool descriptions literal; no instructions to the agent inside them.
AST04

Cost to the agent

Instructions loaded
≈69 tok
1 file · 81 in bundle
Tool list per prompt
≈0 tok
0 tools · 0 per tool
Handshake
no reply
launch to tools/list, stdio
Undocumented tools
0
description under 20 chars · avg 0

Tokens estimated at four characters each. The tool list is re-read by the agent on every turn, so it is the number to compare between servers that do the same job: ranked across the index.

Known vulnerabilities

No advisories in OSV for pdbe-mcp-server@2.0.1 as of 7 min ago. This is the package itself, not its dependencies.