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Protein MCP Server vs Mirobody

A side-by-side look at the Protein MCP Server and Mirobody MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.

Protein MCP Server logoProtein MCP ServerBiology & BioinformaticsFederated protein structure & function across experimental (PDB) and predicted (AlphaFold) models.49FairAuth: no auth requiredMirobody logoMirobodyBiology & BioinformaticsTurn scattered health data into answers you can trace. Self-hosted AI health data engine for lab reports, wearables and genetics, with a built-in MCP server. Run it with Docker and one LLM key, or keep every model local on llama.cpp.51GoodAuth: not declared

Verdict: choose Protein MCP Server for biology & bioinformatics work; choose Mirobody for biology & bioinformatics. You can also run both side by side in one mcpServers block.

Which MCP server should you choose?

Protein MCP Server logoChoose Protein MCP Server when

  • You need dedicated capabilities in the Biology & Bioinformatics domain.
  • Its auth model fits you: No auth required.
  • You want tools like protein_search_structures, protein_get_structure, protein_find_similar.
Explore Protein MCP Server

Mirobody logoChoose Mirobody when

  • You need dedicated capabilities in the Biology & Bioinformatics domain.
Explore Mirobody

Feature & specification comparison

Rows where the two servers differ are marked.

SpecProtein MCP Server logoProtein MCP ServerMirobody logoMirobody
CategoryBiology & BioinformaticsBiology & Bioinformatics
Quality signal49/100 · Fair51/100 · Good
Install commandNot confirmed yetNot confirmed yet
Transport——
AuthNo auth requiredNot declared
PricingFreeBYOK (pay the provider)
Required env varsNone listedNone listed
Verified ownerCommunity listingCommunity listing
GitHub stars61,389
Directory activity 1 views 0 installs 0 upvotes 3 views 0 installs 0 upvotes
Tools7Not listed
Full listingView Protein MCP Server View Mirobody

Tools & capabilities

Protein MCP Server tools 7

  • protein_search_structuresSearch experimental and predicted structures by text, sequence, or organism/method/resolution, with optional facets
  • protein_get_structureFetch metadata and coordinate URLs for experimental, predicted, or best-available structures
  • protein_find_similarFind sequence homologs (RCSB mmseqs2) or fold homologs (Foldseek)
  • protein_track_ligandsResolve ligands to component IDs, find structures containing one, or map its binding site
  • protein_compare_structuresAlign structures with TM-align or jFATCAT, against a reference or all pairs
  • protein_analyze_collectionProfile the PDB as counts, histograms, timelines, and cross-tabs
  • protein_get_annotationsFetch UniProt features and variants plus InterPro domains with GO terms

Mirobody 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.

Protein MCP Server

No confirmed install command for Protein MCP Server yet — follow the setup steps linked from its listing page rather than a guessed package name.

Mirobody

No confirmed install command for Mirobody yet — follow the setup steps linked from its listing page rather than a guessed package name.

Frequently asked questions

Protein MCP Server is categorized under Biology & Bioinformatics and uses an install path we have not confirmed yet. Mirobody belongs to Biology & Bioinformatics and uses an install path we have not confirmed yet. Pick Protein MCP Server for biology & bioinformatics work and Mirobody for biology & bioinformatics.

Neither server has a confirmed install command yet, so we don't publish a guessed config. Follow each project's own setup instructions, linked from its listing page.

Protein MCP Server is listed as free. Auth: no auth required. Mirobody is bring-your-own-key: usage is billed by the API provider you supply a key for. 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 protein-mcp-server and mirobody as separate keys in the same mcpServers object, and your assistant will call tools from either one.

On AllMCPs, Protein MCP Server has a quality signal of 49/100 (Fair) with 1 views, 0 installs and 6 GitHub stars. Mirobody has 51/100 (Good) with 3 views, 0 installs and 1,389 GitHub stars.

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