Emdb Mcp

io.github.mrfentmen由 GitHub 帳號 mrfentmen 發布v1.0.1更新於 Nov 6, 2026

EBI Electron Microscopy Data Bank: search cryo-EM maps and read resolution and method

已驗證STDIO僅桌面知識與記憶

概覽

AI 產生的概覽

檢索 EBI 電子顯微鏡資料庫(EMDB),讀取冷凍電鏡條目的解析度、方法與關聯的 PDB 交叉參照。

可以做什麼
  • 以標題、作者或樣品等自由文字檢索 EMDB 冷凍電鏡條目
  • 讀取單一條目的標題、解析度、方法、作者、存放日期與主要引用文獻
  • 列出條目紀錄中附帶的 PDB 交叉參照
適用情境
適合需要快速、唯讀查詢 EMDB 公開冷凍電鏡圖譜中繼資料的情境,例如確認某個結構的解析度或方法,或找出與某筆 EMDB 紀錄關聯的 PDB 條目。
執行需求
以本機 stdio 程序執行,從 npm 套件 @mrfentmen/emdb-mcp 安裝,需要 Node.js 與 npm。未宣告 API 金鑰、環境變數或請求標頭;透過網路讀取 EMDB 公開資料。
安裝前請注意
僅提供唯讀查詢工具,未宣告寫入、付費或憑證需求。資料來自第三方公開檔案庫,中繼資料可能不完整或過時,應與原始紀錄核對。

安裝

在 SourceWeft 中

  1. 開啟 儀表板中的 Emdb Mcp,將其新增到工作區。
  2. 為需要使用其工具的對話啟用該服務。

Desktop only,透過 STDIO。 STDIO 服務會啟動本機處理程序,因此需要 SourceWeft 桌面主機。

其他 MCP 客戶端

參照 儲存庫 中的啟動說明。

README

awesome-servers

One repo for three families of servers, each subtree keeping its own layout and tooling so it can still be built, run and published on its own.

SubtreeWhat it holdsRun one
mcp/338 TypeScript MCP servers, plus 1107 published packages in published/cd mcp/servers/<slug> && npm install && npm run build
acp/79 Python ACP agentspython3 acp/agents/<name>/agent.py
a2a/37 Python A2A servers plus the shared a2a_kitpython3 a2a/servers/<name>/server.py
watchd/a threshold watcher that runs the feeds between editor sessionspython3 watchd/watchd.py --config conditions.json --loop
site/the published site: registry with search, the public-feed atlas, watchd planshttps://mrfentmen.github.io/awesome-servers/

Most servers read public data with no key of their own; the ones wrapping a vendor API take that vendor's key. Nothing in this repo asks a caller to pay. On 2026-10-17 the licence machinery was removed for good: the per-tool src/license.ts gates are gone from the MCP servers, and the A2A and ACP trees no longer carry the hosted licence-gateway half — the skills that used it now answer with an explicit not-implemented stub. Nothing here asks a caller to pay, and nothing they run is refused with a buy link.

Nothing here is generated: each subtree's README says what its servers read, and every server has its own unit tests (mcp/servers/<slug>/tests, acp/agents/<name>/tests, a2a/servers/<name>/tests) plus a live smoke check (tools/smoke*.py, a2a/tools/smoke_all.py).

Novel and original

Nearly all of this is first-of-its-kind work, not a port of an existing catalogue. Before each server or agent was built, it was checked against the official tool lists (the MCP registries, agentclientprotocol.com's agent list and registry) and a live GitHub search for the same domain, and the research logs record what was found and why it still counted as missing — see mcp/MISSING.md, acp/MISSING.md and a2a/docs/. Highlights:

  • The MCP side holds TypeScript servers, one npm package each, and 1039 published packages under published/; mcp/MISSING.md documents the check that preceded every build: what was searched, what was skipped and why the domain still counted as uncovered.
  • On the ACP side there were zero domain agents before this repo — every agent on the official list was a coding agent. These 79 Python agents are the first non-coding ACP agents, and several use protocol surfaces no other agent uses in production (session/request_permission for dataset reads, fs/write_text_file for a briefing file, session/cancel for a conditional watch, image content blocks, a live SSE push feed), each proved-unused in the wild by search at build time. Two more firsts carry their own proof: the orchestrator is an agent whose feeds are agents — it spawns sibling repo agents as real ACP child processes and merges their answers — and the nyc pack is the first multi-agency city surface.
  • acp/MISSING.md doubles as the public-feed atlas: every keyless feed probed live, with its date, what it answered and whether it still works. The published site renders that table at https://mrfentmen.github.io/awesome-servers/atlas.html.
  • The pattern across all three subtrees is the same thesis: wrap one real, keyless public dataset, answer honestly about what the feed did and did not say, and keep the whole thing small, tested and self-contained.

Publishing

  • MCP servers publish from mcp/servers/<slug> (its own package.json, version and README).
  • ACP and A2A servers are repo-run today (Python, no packaging step).

Built on top of it

Creatures that use this corpus as their world live in the sibling repo mrfentmen/superagents (public, with its own claim-check in MISSING.md):

  • polymath — routes your question to the most fitting agents of this repo, spawns each as a real ACP child process, and merges the answers into one brief with per-row citations; a sibling that fails appears as a named row, never silence. Its registry is a data file and its ranking is deterministic word-scoring, not a model opinion.
  • sentry — one plain sentence ("watch air quality in Denver over 150") becomes a tracked watch: a permission-asked protocol write produces the conditions file this repo's watchd/ obeys unchanged, plus the activation lines. Checks it can author today: air thresholds, quake magnitudes within a radius, river gauges at flood stage.
  • fedora hat guy — the persona agent in his own repo mrfentmen/fedora-hat: says "never miss" and means it — one sentence installs the full crown of watches (air + quakes, gauge-named flood) in one permissioned write, and your other questions are forwarded to the siblings above with every row cited.
  • instink — the instinct agent in his own repo mrfentmen/instink: compiles a skill into a reflex — a matcher plus the answer it fires, with hit/miss counters and honest promotion/demotion. The skill doc stays one step away, never deleted.
  • contextink — the context agent in his own repo mrfentmen/contextink: you say "do this" and it acquires the context from the repo, git, and recent files so you don't have to explain it; asks only the minimal high-information-gain questions when acquisition fails.
  • rewind — the replay agent in his own repo mrfentmen/rewind: replays agent runs and mutates one variable to see what would have happened. Replay + mutate + diff for agent traces.
  • scopink — the scope agent in his own repo mrfentmen/scopink: checks if an action is within the scope of what was asked. Detects scope creep in agent plans.
  • curious — the curiosity agent in his own repo mrfentmen/curious: proactively seeks information it doesn't have. Scans for knowledge gaps, seeks answers, learns facts.
  • bored — the idle agent in his own repo mrfentmen/bored: uses idle time productively. Consolidates memories, explores areas, prepares for tasks.

Point the polymath at a checkout of this repo with AWESOME_SERVERS_HOME=$PWD/awesome-servers and it federates across the two repos live.

Published snapshot (published/)

published/ holds one directory per npm package, byte-for-byte what the registry serves: 1039 packages, every version matching npm latest.

  • published/INDEX.md is generated from the tree by python3 scripts/index-published.py.
  • scripts/sync-published-snapshot.py re-downloads every package from npm; run it only when every local fix has been published, because it overwrites dist/ from the tarballs.
  • One package carries a licence gate (MCP_LICENSE_KEY): @mrfentmen/vg-resource-mcp. Another 495 still ship tools that answer Not yet implemented; published/INDEX.md lists every one of them.
  • Every package links to this repo (mrfentmen/awesome-servers) as its source.

servers/ holds the older per-server source that predates the snapshot. Where the two disagree, published/ is what users actually install.

來源:README.md,提交 ee04f93

工具

3

search_entries

Search EMDB cryo-EM entries by free text (title, authors, sample).

輸入參數limitquery必填

entry_detail

One EMDB entry: title, resolution, method, authors, deposition date and the primary citation.

輸入參數emdbId必填

entry_pdbs

The PDB cross-references attached to an EMDB entry, from the entry record.

輸入參數emdbId必填

版本歷史

1
  1. v1.0.1最新Oct 29, 2026

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