protein-mcp-server
https://protein.caseyjhand.com/mcp ↗
Description
Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models.
What our measurements say
protein-mcp-server is a remote MCP server published at protein.caseyjhand.com. It has been probed 6 times since 9/10/2026. It answered in 6 of them (100.0%), a near-uninterrupted record. Median response time is 874 ms, a delay an agent will notice. It offers a narrow, focused set of 7 tools. On the protocol side it speaks the 2026-07-28 stateless spec.
Agent readability score
Can an LLM agent pick the right tool here — names, descriptions and parameter clarity are assessed.
Agent readability score
Strengths
- Comprehensive coverage of structural biology tasks from search to comparison
- Advanced support for asynchronous jobs and polling via tickets/UUIDs
- Clear distinction between experimental and predicted model workflows
Weaknesses
- Severe text truncation in almost all tool descriptions, cutting off critical instructions
- Lack of explicit parameter types (string, int, enum) and requirement indicators
- High cognitive load due to dense, unformatted text blocks
protein_search_structures— Truncated description prevents full understanding of facet usage.protein_get_structure— Truncated description and lack of parameter type definitions.protein_find_similar— Incomplete instructions regarding the asynchronous ticket-based workflow.protein_track_ligands— Description ends abruptly, losing context on ligand matching.protein_compare_structures— Truncated description regarding error degradation behavior.protein_get_annotations— Truncated description regarding chain selection logic.
Verdict
Event narrative
Risk: medium
- 2026-09-10T21:16:35.016Z — Server in 'auth-gated' era with no compliance score · Initial phase without compliance metrics
- 2026-09-11T07:35:54.413Z — Transitioned to 'dual' era with 100 compliance score · Achieved full compliance after transition
Advice
Schema compliance
tools/list structure, inputSchema validity, and a functional smoke test — the components of the 0-100 score.
- tools/list schema valid
- inputSchema is valid JSON Schema
- Smoke test not run this round
- Cold-start: cold 144ms → warm 163ms (penalty 0ms)
Availability history
Event log
Derived by comparing consecutive probes — changes in era, protocol version, build and reachability.
- Server build: — → 0.8.0
- Supported versions: — → 2026-07-28
- Era changed: Auth-gated → Dual-era
- Added to watch — era: Auth-gated
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