Protein MCP Server vs Server Everything
A side-by-side look at the Protein MCP Server and Server Everything MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.
Verdict: choose Protein MCP Server for biology & bioinformatics work; choose Server Everything for other tools and integrations as a local process. You can also run both side by side in one mcpServers block.
Which MCP server should you choose?
Choose 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.
Choose Server Everything when
- You need dedicated capabilities in the Other Tools and Integrations domain.
- You prefer a local stdio subprocess transport.
- Its auth model fits you: No auth required.
- You want tools like
echo, get-annotated-message, get-env.
Feature & specification comparison
Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Biology & Bioinformatics | Other Tools and Integrations |
| Quality signal | 49/100 · Fair | 73/100 · Great |
| Install command | Not confirmed yet | Confirmed |
| Transport | — | Local subprocess (stdio) |
| Auth | No auth required | No auth required |
| Pricing | Free | Free |
| Required env vars | None listed | None listed |
| Verified owner | Community listing | Community listing |
| GitHub stars | 6 | 91,547 |
| Directory activity | 1 views 0 installs 0 upvotes | 10 views 0 installs 0 upvotes |
| Tools | 7 | 16 |
| Full listing | View Protein MCP Server | View Server Everything |
Tools & capabilities
Protein MCP Server tools 7
protein_search_structuresSearch experimental and predicted structures by text, sequence, or organism/method/resolution, with optional facetsprotein_get_structureFetch metadata and coordinate URLs for experimental, predicted, or best-available structuresprotein_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 siteprotein_compare_structuresAlign structures with TM-align or jFATCAT, against a reference or all pairsprotein_analyze_collectionProfile the PDB as counts, histograms, timelines, and cross-tabsprotein_get_annotationsFetch UniProt features and variants plus InterPro domains with GO terms
Server Everything tools 16
echoEchoes back the input stringget-annotated-messageDemonstrates how annotations can be used to provide metadata about content.get-envReturns all environment variables, helpful for debugging MCP server configurationget-header-paramsReturns its region argument and the Mcp-Param-Region HTTP header it arrived in. Demonstrates x-mcp-header (a 2026-07-28 Streamable HTTP client mirrors the argument into the header) and JSON Schema 2020-12 input and output schemas.get-resource-linksReturns up to ten resource links that reference different types of resourcesget-resource-referenceReturns a resource reference that can be used by MCP clientsget-structured-contentReturns structured content along with an output schema for client data validationget-sumReturns the sum of two numbersget-tiny-imageReturns a tiny MCP logo image.gzip-file-as-resourceCompresses a single file using gzip compression. Depending upon the selected output type, returns either the compressed data as a gzipped resource or a resource link, allowing it to be downloaded in a subsequent request: during the current session for a 2025-era client, or for ten minutes at a minted URI on protocol version 2026-07-28.trigger-list-changedSends a notifications/<list>/list_changed for the tool, prompt or resource list. On protocol version 2026-07-28 it is delivered on each subscriptions/listen stream that asked for that list; a 2025-era client receives it unsolicited.trigger-log-messagesSends one log message at each logging level during the call. On protocol version 2026-07-28 only the messages at or above the level the request names in _meta (io.modelcontextprotocol/logLevel) are sent, and none if it names no level; a 2025-era client gets those at or above the level it set with logging/setLevel. Deprecated: logging is deprecated as of protocol version 2026-07-28.- +4 more on 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.
Server Everything
{
"mcpServers": {
"modelcontextprotocol-server-everything": {
"command": "npx",
"args": [
"-y",
"@modelcontextprotocol/server-everything"
]
}
}
}
Frequently asked questions
Protein MCP Server is categorized under Biology & Bioinformatics and uses an install path we have not confirmed yet. Server Everything belongs to Other Tools and Integrations and uses a local stdio subprocess. Pick Protein MCP Server for biology & bioinformatics work and Server Everything for other tools and integrations.
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. Protein MCP Server has no confirmed install command yet — follow its own setup instructions.
Protein MCP Server is listed as free. Auth: no auth required. Server Everything 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 protein-mcp-server and modelcontextprotocol-server-everything 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. Server Everything has 73/100 (Great) with 10 views, 0 installs and 91,547 GitHub stars.