Alphafold
Server Details
AlphaFold DB MCP — predicted protein structures.
- Status
- Healthy
- Last Tested
- Transport
- Streamable HTTP
- URL
- Repository
- pipeworx-io/mcp-alphafold
- GitHub Stars
- 0
- Server Listing
- mcp-alphafold
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Tool Definition Quality
Average 4.5/5 across 35 of 35 tools scored. Lowest: 2.9/5.
Many tools have highly overlapping purposes, especially the ask_pipeworx family (ask_pipeworx, ask_pipeworx_beta, ask_pipeworx_grounded) which all route to the same data sources with minor differences. Similarly, there are four polymarket-specific tools (bet_research, polymarket_arbitrage, polymarket_edges, polymarket_edge_tracker) that target the same prediction market but with different angles, making it hard for an agent to choose correctly without deep understanding.
Tool names exhibit no consistent pattern: some use snake_case (ai_visibility_check, recent_alerts), some camelCase (bet_research, discover_tools), and one is a verb_noun pair (generate_llms_txt). Others like ask_pipeworx are verb_compound_noun. The mix of conventions creates confusion and lacks predictability.
With 35 tools, the server is cluttered. Only about 4-5 tools relate to the promised AlphaFold domain (prediction, uniprot, summary, annotations); the rest cover unrelated areas like company research, prediction markets, and utility functions. This mismatch makes the tool count feel inflated and inappropriate for the server's stated purpose.
For an AlphaFold-focused server, the tool surface is severely incomplete. It offers only basic retrieval of predictions and annotations. Missing are capabilities for batch predictions, sequence alignment, structure comparison, visualization, or integration with other bioinformatics tools. Meanwhile, the vast majority of tools address entirely different domains, leaving the core function underrepresented.
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