Pdbe vs Togomcp
A side-by-side look at the Pdbe and Togomcp MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.
T
TogomcpBiology & BioinformaticsMCP server for life-science knowledge graphs36FairAuth: api key requiredVerdict: choose Pdbe for biology & bioinformatics work as a local process; choose Togomcp for biology & bioinformatics. 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.
TChoose Togomcp when
- You need dedicated capabilities in the Biology & Bioinformatics domain.
- Its auth model fits you: API key required.
- You have the keys it needs:
NCBI_API_KEY.
Feature & specification comparison
Rows where the two servers differ are marked.
| Spec | T Togomcp | |
|---|---|---|
| Category | Biology & Bioinformatics | Biology & Bioinformatics |
| Quality signal | 51/100 · Good | 36/100 · Fair |
| Install command | Confirmed | Not confirmed yet |
| Transport | Local subprocess (stdio) | — |
| Auth | Not declared | API key required |
| Pricing | Not declared | Not declared |
| Required env vars | None listed | NCBI_API_KEY |
| Verified owner | Community listing | Community listing |
| GitHub stars | 0 | 19 |
| Directory activity | 2 views 0 installs 0 upvotes | 0 views 0 installs 0 upvotes |
| Tools | 3 | Not listed |
| Full listing | View Pdbe | View Togomcp |
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".
Togomcp tools
No tool names declared yet. Check the project README from the listing page.
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"
]
}
}
}
Togomcp
No confirmed install command for Togomcp yet — follow the setup steps linked from its listing page rather than a guessed package name.
Frequently asked questions
Pdbe is categorized under Biology & Bioinformatics and uses a local stdio subprocess. Togomcp belongs to Biology & Bioinformatics and uses an install path we have not confirmed yet. Pick Pdbe for biology & bioinformatics work and Togomcp for biology & bioinformatics.
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. Togomcp has no confirmed install command yet — follow its own setup instructions.
Pdbe has no declared pricing — check the project's own site. Togomcp has no declared pricing — check the project's own site. Auth: api key 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 togomcp 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. Togomcp has 36/100 (Fair) with 0 views, 0 installs and 19 GitHub stars.