Pdbe vs Exa MCP Server
A side-by-side look at the Pdbe and Exa MCP Server MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.
Verdict: choose Pdbe for biology & bioinformatics work as a local process; choose Exa MCP Server for search & data extraction as a local process. You can also run both side by side in one mcpServers block.
Which MCP server should you choose?
Choose Pdbe when
- You need dedicated capabilities in the Biology & Bioinformatics domain.
- You prefer a local stdio subprocess transport.
- You want tools like
get_summary, get_molecules, uniprot_mappings.
Choose Exa MCP Server when
- You need dedicated capabilities in the Search & Data Extraction domain.
- You prefer a local stdio subprocess transport.
- Its auth model fits you: No auth required.
- You want tools like
web_search_exa, web_fetch_exa.
Feature & specification comparison
Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Biology & Bioinformatics | Search & Data Extraction |
| Quality signal | 51/100 · Good | 73/100 · Great |
| Install command | Confirmed | Confirmed |
| Transport | Local subprocess (stdio) | Local subprocess (stdio) |
| Auth | Not declared | No auth required |
| Pricing | Not declared | Free |
| Required env vars | None listed | None listed |
| Verified owner | Community listing | Community listing |
| GitHub stars | 0 | 5,162 |
| Directory activity | 2 views 0 installs 0 upvotes | 11 views 0 installs 0 upvotes |
| Tools | 3 | 2 |
| Full listing | View Pdbe | View Exa MCP Server |
Tools & capabilities
Pdbe tools 3
get_summaryPDBe (Protein Data Bank in Europe, EBI): get a PDB entry summary — title, experimental method, release date, source organism, and entity counts (polypeptide/ligand/water/...). Keyless. The EBI counterpart to RCSB PDB. Pass a 4-char PDB id like "1cbs".get_moleculesPDBe (EBI): list the molecules/entities in a PDB structure — proteins, nucleic acids, and ligands, each with entity_id, molecule_type, name, and chain length. Keyless. Pass a 4-char PDB id like "1cbs".uniprot_mappingsPDBe (EBI): SIFTS cross-database mapping of a PDB structure to UniProt — for each UniProt accession, the matching chains and residue range. Curated cross-database mappings unique to EBI. Keyless. Pass a 4-char PDB id like "1cbs".
Exa MCP Server tools 2
web_search_exaSearch the web for any topic and get clean, ready-to-use content. Best for: Finding current information, news, facts, people, companies, or answering questions about any topic. Returns: Clean text content from top search results. Query tips: describe the ideal page, not keywords. "blog post comparing React and Vue performance" not "React vs Vue". Use category:people / category:company to search through Linkedin profiles / companies respectively. If highlights are insufficient, follow up with web_fetch_exa on the best URLs.web_fetch_exaRead a webpage's full content as clean markdown. Use after web_search_exa when highlights are insufficient or to read any URL. Best for: Extracting full content from known URLs. Batch multiple URLs in one call. Returns: Clean text content and metadata from the page(s).
Ready-to-paste client configs
Paste either block (or both) into your client config, e.g. claude_desktop_config.json or ~/.cursor/mcp.json. We only show a config when the install command is confirmed.
Pdbe
{
"mcpServers": {
"pdbe": {
"command": "npx",
"args": [
"-y",
"@pipeworx/mcp-pdbe"
]
}
}
}
Exa MCP Server
{
"mcpServers": {
"exa-labs-exa-mcp-server": {
"command": "npx",
"args": [
"-y",
"exa-mcp-server"
]
}
}
}
Frequently asked questions
Pdbe is categorized under Biology & Bioinformatics and uses a local stdio subprocess. Exa MCP Server belongs to Search & Data Extraction and uses a local stdio subprocess. Pick Pdbe for biology & bioinformatics work and Exa MCP Server for search & data extraction.
Copy the mcpServers block from the config section on this page into your client's config (for example claude_desktop_config.json or ~/.cursor/mcp.json), then fully restart the client.
Pdbe has no declared pricing — check the project's own site. Exa MCP Server is listed as free. Auth: no auth required. If a server needs environment variables such as API keys, define them under the env key in your client's MCP config.
Yes. MCP clients support multiple servers: add pdbe and exa-labs-exa-mcp-server as separate keys in the same mcpServers object, and your assistant will call tools from either one.
On AllMCPs, Pdbe has a quality signal of 51/100 (Good) with 2 views, 0 installs and 0 GitHub stars. Exa MCP Server has 73/100 (Great) with 11 views, 0 installs and 5,162 GitHub stars.