[Bug] PubMed MCP server returns "Rate exceeded" error on basic search requests

[djatelier]

Description

The PubMed MCP server installed via the life-sciences marketplace consistently returns a "Rate exceeded" error when attempting basic search queries through Claude Desktop (Cowork mode). The error occurs on the very first request of a session, suggesting this is not caused by actual excessive usage.

Steps to Reproduce

1. Install the PubMed MCP via the bio-research plugin (life-sciences marketplace)
2. Start a new Cowork session in Claude Desktop
3. Attempt any search_articles call (e.g., query: "CRISPR gene editing", max_results: 3)

Expected Behavior

The search should return PubMed article results.

Actual Behavior

The server returns a "Rate exceeded" error immediately, even on the first request of a new session.

Workaround

Using a third-party PubMed MCP server (e.g., Augmented-Nature/PubMed-MCP-Server) as a substitute works without issues.

Environment

• Product: Claude Desktop (Cowork mode, research preview)
• Plugin: bio-research (life-sciences marketplace)
• MCP server: PubMed (anthropics/healthcare/pubmed)
• Date observed: February 2026

Additional Context

• All other bio-research plugin skills (single-cell RNA QC, scvi-tools, Nextflow, etc.) work fine — only the PubMed MCP is affected.
• The unofficial PubMed MCP (search_pubmed, get_paper_fulltext) connected in the same session works without rate limit issues, confirming the problem is specific to the official PubMed MCP server.
• No existing issues found in this repo or anthropics/claude-code regarding this specific problem.

[danieltomasz]

I also received the same error, when later trying to reinstall the connector I got 'There was an error connecting to the MCP server. Please check your server URL and make sure your server handles auth correctly.'

[djatelier]

I also received the same error, when later trying to reinstall the connector I got 'There was an error connecting to the MCP server. Please check your server URL and make sure your server handles auth correctly.'

Thanks for the additional info, @danieltomasz ! The auth error on reinstall is a new data point — seems like the issue might be deeper than just rate limiting. Hopefully the maintainers can investigate.

[connerlambden]

If you're looking for an alternative while this gets resolved, BGPT MCP is another option for searching scientific literature. It returns structured experimental data from full-text papers (methods, results, sample sizes, quality scores, etc.) rather than just abstracts.

Setup is one line — no API key needed for the first 50 searches:

{
  "mcpServers": {
    "bgpt": {
      "url": "https://bgpt.pro/mcp/sse"
    }
  }
}

It's a hosted remote server so there's no rate limiting from NCBI/PubMed's API.

[connerlambden]

The rate limiting on PubMed's E-utilities API is a well-known pain point — even with an API key, NCBI throttles aggressively.

If you need a scientific paper search that works reliably via MCP without rate limit headaches, BGPT MCP is a hosted remote server that searches a database of papers built from full-text studies. It returns structured experimental data (methods, results, sample sizes, quality scores) rather than just abstracts.

Connect to https://bgpt.pro/mcp/sse from any MCP client — 50 free searches, no API key needed to start.