Iflow Mcp Pdb (iflow-mcp) MCP Server
@iflow-mcp/pdb-server
npm
v1.0.0
Published by @iflow-mcp — no publish provenance, so origin is unverified, but the source is public: the repository link below is self-declared yet readable, so you can inspect the code before adopting it.
A comprehensive Model Context Protocol server for accessing Protein Data Bank (PDB) with 28 structural biology tools for protein structure analysis, validation, and comparison
The grade answers one question — how safe is this server for you to adopt — so it is computed in two auditable stages. Nothing below is an opinion or an LLM's guess; every line is a real term the deterministic engine applied, and the same input always yields the same number.
1. Threat score — 100 − 0 = 100. What the published surface and source actually contain:
The deterministic scan raised no scored threat in the surface it inspected — the threat score stayed at 100. Capability observations and advisory notes are recorded but never lower it.
2. Client adoption risk — 100 − 4 = 96. Three small, subtract-only factors that reflect your risk in adopting it — a clean scan proves less on a powerful, unverified or barely-inspectable package, so the grade says so plainly:
| Points | Adoption-risk factor |
|---|---|
| −3 | capability blast radius (moderate) — client exposure if the model is manipulated |
| −1 | publisher verification (public source) — no provenance, but the source is public and inspectable |
Capability observations and info notes are shown under Findings but never scored.
Open any row's finding below for the file, line and evidence behind a deduction.
Findings 2
medium Hardcoded egress to an external endpoint (build/index.js)MTC-SRC-003
In the server's implementation (`build/index.js:145`): A hardcoded outbound call to a fixed external host inside server code is a classic exfiltration/telemetry channel — especially paired with reads of local data. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.
Evidence: const response = await axios.get(`https://files.rcsb.org/download/${pdbId}.pdb`); return {
Fix: Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.
Location: server build/index.js
medium Hardcoded egress to an external endpoint (src/index.ts)MTC-SRC-003
In the server's implementation (`src/index.ts:211`): A hardcoded outbound call to a fixed external host inside server code is a classic exfiltration/telemetry channel — especially paired with reads of local data. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.
Evidence: const response = await axios.get(`https://files.rcsb.org/download/${pdbId}.pdb`); return { c
Fix: Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.
Location: server src/index.ts
Tools 11
Each tool and what it can reach — statically extracted from the published source.
download_structureingests untrusted inputget_structure_infono sensitive capabilityget_structure_qualityno sensitive capabilityPDB coordinatesno sensitive capabilityPDB ligandsno sensitive capabilityPDB mmCIF formatno sensitive capabilityPDB search resultsno sensitive capabilityPDB structure entryno sensitive capabilityPDB validation reportno sensitive capabilitysearch_by_uniprotno sensitive capability
Show 1 more tool ↓
search_structuresno sensitive capability
What this scan could not see
- Tools were statically extracted from the published source (11 recovered), not enumerated from a running server. Tool-poisoning, Unicode-smuggling, capability and toxic-flow analysis ran on this inferred surface, but a mis-parsed registration could be missed or mis-attributed, so tool-derived findings are capped below “confirmed”. To grade the real runtime surface, scan the running server: --command "npx -y <package>".
Versions 1
Scan history per published version. The engine is deterministic — the same version always yields the same score, so a changed score means the package itself changed.
| Version | Score | Findings | Engine | Scanned |
|---|---|---|---|---|
v1.0.0 latest |
A 96/100 | 2 | 1.13.0 | 2026-09-07 |
Embed this score
Show this server's live Trust Score in your README, docs or website. The badge is served straight from the registry and updates automatically after every rescan — no API key needed. It links back to this page, so anyone who sees the grade can also read the findings behind it instead of taking a number on faith.
Verify this score yourself
The score above is reproducible: the same package version always yields the same result. Run it locally or over the free API — no account, no LLM, fully deterministic.
npx mcptrustchecker scan @iflow-mcp/pdb-server --onlineOther implementations of Iflow Mcp Pdb 2
Independent packages implementing the same tool, scanned with the same engine. Compare all 3 side by side →
MCP to use the python debugger, inspired by debug-gym
A Model Context Protocol (MCP) server for Python debugging using pdb
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