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PDB-MCP-Server

A Model Context Protocol (MCP) server that provides access to the Protein Data Bank (PDB) - the worldwide repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.

→ Augmented-Nature/PDB-MCP-Server· listed on github_topic
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// key findings
⚠️
Known vulnerabilities in dependencies: 16 high
Affects packages this MCP installs at runtime. Upgrade or remove the affected dependency.
✅
No credential exfiltration, no sensitive file access, no obfuscation
Static analysis found nothing flowing your secrets to unexpected places.
✅
Open source with a license and README
Anyone can audit the code, the license is declared, and the publisher documents what it does.
// known CVEs in dependencies16 high12 low

Disclosed vulnerabilities in this server's declared npm dependencies (via OSV). Whether each is reachable depends on the installed versions.

high@modelcontextprotocol/sdk@0.5.0GHSA-8r9q-7v3j-jr4g

Anthropic's MCP TypeScript SDK has a ReDoS vulnerability

high@modelcontextprotocol/sdk@0.5.0GHSA-w48q-cv73-mx4w

Model Context Protocol (MCP) TypeScript SDK does not enable DNS rebinding protection by default

highaxios@1.6.0GHSA-35jp-ww65-95wh

axios Vulnerable to Full Man-in-the-Middle via Prototype Pollution Gadget in `config.proxy`

highaxios@1.6.0GHSA-3g43-6gmg-66jw

axios Vulnerable to Credential Theft and Response Hijacking via Prototype Pollution Gadget in Config Merge

highaxios@1.6.0GHSA-43fc-jf86-j433

Axios is Vulnerable to Denial of Service via __proto__ Key in mergeConfig

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// full audit trail
The full breakdown of what we checked, the deductions that landed, the network hosts, the dependency advisories, and concrete fix guidance is available to verified publishers.
// improvement guidance — verified publishers only
We have 4 concrete improvements we can share with the publisher of this MCP. Each comes with specific guidance to raise the trust score.
// embed badge in your README
[![M8ven Score](https://m8ven.ai/badge/mcp/augmented-nature-pdb-mcp-server-1upzfo)](https://m8ven.ai/mcp/augmented-nature-pdb-mcp-server-1upzfo)
commit: d7f2d258494877492f824a299134f30b8b76e950
code hash: b4ac8371bebf75056cac671b70f222205ac8aa0aea778d476f89a79db1ed7dd5
verified: 6/15/2026, 1:12:16 PM
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