@cyanheads/protein-mcp-server 0.1.3 → 0.1.4
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/AGENTS.md +2 -2
- package/CLAUDE.md +2 -2
- package/README.md +2 -2
- package/changelog/0.1.x/0.1.4.md +15 -0
- package/dist/index.js +1 -9
- package/dist/index.js.map +1 -1
- package/package.json +3 -3
- package/server.json +4 -4
package/AGENTS.md
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@@ -1,7 +1,7 @@
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# Developer Protocol
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**Server:** protein-mcp-server
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**Version:** 0.1.
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**Version:** 0.1.4
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.9`
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**Engines:** Bun ≥1.3.0, Node ≥24.0.0
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**MCP SDK:** `@modelcontextprotocol/sdk` ^1.29.0
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resources: [pdbSummaryResource, afSummaryResource],
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prompts: [],
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landing: { requireAuth: false }, // public, keyless data server
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instructions: 'protein-mcp-server — federated protein structure &
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instructions: 'protein-mcp-server — federated protein structure & annotation over experimental (PDB) and predicted (AlphaFold) structures.',
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setup(core) { /* init the six provider services */ },
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});
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```
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package/CLAUDE.md
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# Developer Protocol
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**Server:** protein-mcp-server
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**Version:** 0.1.
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**Version:** 0.1.4
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.9`
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**Engines:** Bun ≥1.3.0, Node ≥24.0.0
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**MCP SDK:** `@modelcontextprotocol/sdk` ^1.29.0
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@@ -171,7 +171,7 @@ await createApp({
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resources: [pdbSummaryResource, afSummaryResource],
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prompts: [],
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landing: { requireAuth: false }, // public, keyless data server
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instructions: 'protein-mcp-server — federated protein structure &
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instructions: 'protein-mcp-server — federated protein structure & annotation over experimental (PDB) and predicted (AlphaFold) structures.',
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setup(core) { /* init the six provider services */ },
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});
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```
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package/README.md
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<div align="center">
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<h1>@cyanheads/protein-mcp-server</h1>
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<p><b>Federated protein structure &
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<p><b>Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.</b>
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<div>7 Tools • 2 Resources</div>
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</p>
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</div>
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<div align="center">
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[](./CHANGELOG.md) [](./LICENSE) [](https://github.com/users/cyanheads/packages/container/package/protein-mcp-server) [](https://modelcontextprotocol.io/) [](https://www.npmjs.com/package/@cyanheads/protein-mcp-server) [](https://www.typescriptlang.org/) [](https://bun.sh/)
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</div>
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---
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summary: "Narrow the public description and server instructions from 'structure & function' to 'structure & annotation'. No behavior changes."
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breaking: false
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security: false
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---
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# 0.1.4 — 2026-06-23
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Copy refinement. No tool, resource, schema, or behavior changes.
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## Changed
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- **Description** — narrowed from "structure & function" to "structure & annotation" across `package.json`, `server.json`, `manifest.json`, both plugin manifests, and the README tagline. The server federates structure plus UniProt/InterPro/GO annotation, not function research.
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- **`instructions`** — rewritten from a bulleted concatenation to a single prose paragraph with the same narrowed framing; dropped the operator-facing "No API keys required" note, which doesn't belong in agent-facing session context. `AGENTS.md`/`CLAUDE.md` mirrors updated to match.
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- **Dependencies** — `@biomejs/biome` (dev) 2.5.0 → 2.5.1.
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package/dist/index.js
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prompts: [],
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// Public, keyless data server — serve the full inventory to unauthenticated callers.
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landing: { requireAuth: false },
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instructions: 'protein-mcp-server
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'predicted (AlphaFold) structures. No API keys required.\n' +
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'- protein_search_structures: find structures by text, sequence, or organism/method/resolution; optional facet breakdown\n' +
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'- protein_get_structure: fetch metadata + coordinate URLs for PDB IDs or UniProt accessions (batch, partial success)\n' +
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'- protein_find_similar: sequence (mmseqs2) or structure (Foldseek) similarity search\n' +
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'- protein_track_ligands: resolve ligands, find structures containing them, or map binding-site residues\n' +
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'- protein_compare_structures: pairwise TM-align / jFATCAT over 2–10 structures\n' +
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'- protein_analyze_collection: server-side facet distributions and trends over the PDB\n' +
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'- protein_get_annotations: UniProt features + InterPro domains/GO terms',
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instructions: 'protein-mcp-server federates experimental (PDB) and predicted (AlphaFold) protein structures: search structures by text, sequence, or organism/method/resolution (protein_search_structures); fetch metadata and coordinate URLs for PDB IDs or UniProt accessions (protein_get_structure); find sequence or fold homologs via mmseqs2 or Foldseek (protein_find_similar); resolve ligands and map binding-site residues (protein_track_ligands); align 2–10 structures with TM-align or jFATCAT (protein_compare_structures); profile the PDB with server-side facet distributions and trends (protein_analyze_collection); and pull UniProt features plus InterPro domains and GO terms (protein_get_annotations).',
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setup(core) {
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const serverConfig = getServerConfig();
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initRcsbService(core.config, core.storage, serverConfig);
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package/dist/index.js.map
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;;;GAKG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,iBAAiB,EAAE,kBAAkB,EAAE,MAAM,6CAA6C,CAAC;AACpG,OAAO,EACL,iBAAiB,EACjB,iBAAiB,EACjB,WAAW,EACX,cAAc,EACd,YAAY,EACZ,gBAAgB,EAChB,YAAY,GACb,MAAM,yCAAyC,CAAC;AACjD,OAAO,EAAE,oBAAoB,EAAE,MAAM,2CAA2C,CAAC;AACjF,OAAO,EAAE,oBAAoB,EAAE,MAAM,2CAA2C,CAAC;AACjF,OAAO,EAAE,kBAAkB,EAAE,MAAM,uCAAuC,CAAC;AAC3E,OAAO,EAAE,mBAAmB,EAAE,MAAM,yCAAyC,CAAC;AAC9E,OAAO,EAAE,eAAe,EAAE,MAAM,iCAAiC,CAAC;AAClE,OAAO,EAAE,kBAAkB,EAAE,MAAM,uCAAuC,CAAC;AAE3E,MAAM,SAAS,CAAC;IACd,IAAI,EAAE,oBAAoB;IAC1B,KAAK,EAAE,oBAAoB;IAC3B,KAAK,EAAE;QACL,gBAAgB;QAChB,YAAY;QACZ,WAAW;QACX,YAAY;QACZ,iBAAiB;QACjB,iBAAiB;QACjB,cAAc;KACf;IACD,SAAS,EAAE,CAAC,kBAAkB,EAAE,iBAAiB,CAAC;IAClD,OAAO,EAAE,EAAE;IACX,qFAAqF;IACrF,OAAO,EAAE,EAAE,WAAW,EAAE,KAAK,EAAE;IAC/B,YAAY,EACV,
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;;;GAKG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,iBAAiB,EAAE,kBAAkB,EAAE,MAAM,6CAA6C,CAAC;AACpG,OAAO,EACL,iBAAiB,EACjB,iBAAiB,EACjB,WAAW,EACX,cAAc,EACd,YAAY,EACZ,gBAAgB,EAChB,YAAY,GACb,MAAM,yCAAyC,CAAC;AACjD,OAAO,EAAE,oBAAoB,EAAE,MAAM,2CAA2C,CAAC;AACjF,OAAO,EAAE,oBAAoB,EAAE,MAAM,2CAA2C,CAAC;AACjF,OAAO,EAAE,kBAAkB,EAAE,MAAM,uCAAuC,CAAC;AAC3E,OAAO,EAAE,mBAAmB,EAAE,MAAM,yCAAyC,CAAC;AAC9E,OAAO,EAAE,eAAe,EAAE,MAAM,iCAAiC,CAAC;AAClE,OAAO,EAAE,kBAAkB,EAAE,MAAM,uCAAuC,CAAC;AAE3E,MAAM,SAAS,CAAC;IACd,IAAI,EAAE,oBAAoB;IAC1B,KAAK,EAAE,oBAAoB;IAC3B,KAAK,EAAE;QACL,gBAAgB;QAChB,YAAY;QACZ,WAAW;QACX,YAAY;QACZ,iBAAiB;QACjB,iBAAiB;QACjB,cAAc;KACf;IACD,SAAS,EAAE,CAAC,kBAAkB,EAAE,iBAAiB,CAAC;IAClD,OAAO,EAAE,EAAE;IACX,qFAAqF;IACrF,OAAO,EAAE,EAAE,WAAW,EAAE,KAAK,EAAE;IAC/B,YAAY,EACV,srBAAsrB;IACxrB,KAAK,CAAC,IAAI;QACR,MAAM,YAAY,GAAG,eAAe,EAAE,CAAC;QACvC,eAAe,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QACzD,oBAAoB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QAC9D,kBAAkB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QAC5D,kBAAkB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QAC5D,oBAAoB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QAC9D,mBAAmB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;IAC/D,CAAC;CACF,CAAC,CAAC"}
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package/package.json
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{
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"name": "@cyanheads/protein-mcp-server",
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"version": "0.1.
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"version": "0.1.4",
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"mcpName": "io.github.cyanheads/protein-mcp-server",
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"description": "Federated protein structure &
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"description": "Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.",
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"type": "module",
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"main": "dist/index.js",
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"types": "dist/index.d.ts",
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},
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"devDependencies": {
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"@biomejs/biome": "2.5.
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"@biomejs/biome": "2.5.1",
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"@types/node": "26.0.0",
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"depcheck": "^1.4.7",
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"ignore": "^7.0.5",
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package/server.json
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{
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"$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
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"name": "io.github.cyanheads/protein-mcp-server",
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"description": "Federated protein structure &
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"description": "Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models.",
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"repository": {
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"url": "https://github.com/cyanheads/protein-mcp-server",
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"source": "github"
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},
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"version": "0.1.
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"version": "0.1.4",
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"remotes": [
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"type": "streamable-http",
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"registryBaseUrl": "https://registry.npmjs.org",
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"identifier": "@cyanheads/protein-mcp-server",
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"runtimeHint": "node",
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"version": "0.1.4",
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"packageArguments": [
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{
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"type": "positional",
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"registryBaseUrl": "https://registry.npmjs.org",
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"identifier": "@cyanheads/protein-mcp-server",
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"runtimeHint": "node",
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"version": "0.1.4",
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"packageArguments": [
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{
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"type": "positional",
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