pdbe-mcp-server

Provides an MCP (Model Context Protocol) server for working with PDBe (Protein Data Bank in Europe) related resources, exposing PDBe functionality to MCP-capable agents/tools.

Evaluated Apr 04, 2026 (27d ago)
Homepage ↗ Ai Ml mcp pdbe protein-structure bioinformatics agent-tools data-retrieval
⚙ Agent Friendliness
42
/ 100
Can an agent use this?
🔒 Security
38
/ 100
Is it safe for agents?
⚡ Reliability
20
/ 100
Does it work consistently?

Score Breakdown

⚙ Agent Friendliness

MCP Quality
55
Documentation
40
Error Messages
0
Auth Simplicity
50
Rate Limits
20

🔒 Security

TLS Enforcement
50
Auth Strength
30
Scope Granularity
20
Dep. Hygiene
40
Secret Handling
50

No repository/implementation details were provided (e.g., TLS termination, auth, secret management, dependency CVEs). Scores reflect uncertainty rather than confirmed safety properties.

⚡ Reliability

Uptime/SLA
0
Version Stability
30
Breaking Changes
20
Error Recovery
30
AF Security Reliability

Best When

You want an agent-friendly MCP integration to browse and retrieve PDBe-related information as structured tool calls.

Avoid When

You need fully specified REST/OpenAPI contracts, guaranteed auth/rate-limit semantics, or you cannot inspect the server implementation for safety/error handling.

Use Cases

  • • Letting AI agents query PDBe/structural biology data via MCP tools
  • • Automating retrieval of PDB-related metadata for research assistants
  • • Building RAG/workflows that need structured access to PDBe information

Not For

  • • Direct production API usage without MCP support
  • • Use cases requiring strict enterprise auth/compliance guarantees without verifying implementation
  • • Workflows that depend on pagination/search semantics without confirmed tool schemas

Interface

REST API
No
GraphQL
No
gRPC
No
MCP Server
Yes
SDK
No
Webhooks
No

Authentication

OAuth: No Scopes: No

No authentication details were provided in the supplied content, so this is treated as unknown for evaluation scoring.

Pricing

Free tier: No
Requires CC: No

No pricing information was provided.

Agent Metadata

Pagination
none
Idempotent
False
Retry Guidance
Not documented

Known Gotchas

  • ⚠ Tool parameter schemas and response formats may differ from what agents expect unless tool definitions are reviewed.
  • ⚠ Without documented rate limits and error codes, agents may retry too aggressively or mishandle partial failures.

Alternatives

Custom scripts calling PDBe REST APIs directly Generic web search + extraction pipelines (less structured, less reliable) Other MCP servers in the ecosystem that already wrap common bioinformatics endpoints

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API endpoint ↗ Agent guide ↗ Report inaccuracy

Scores are editorial opinions as of 2026-04-04.

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Packages Evaluated
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