@cyanheads/protein-mcp-server 0.1.0

package/LICENSE

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package/README.md

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+<div align="center">
+  <h1>@cyanheads/protein-mcp-server</h1>
+  <p><b>Federated protein structure & function across experimental (PDB) and predicted (AlphaFold) models.</b>
+  <div>7 Tools • 2 Resources</div>
+  </p>
+</div>
+
+<div align="center">
+
+[![Version](https://img.shields.io/badge/Version-0.1.0-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/protein-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/protein-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/protein-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
+
+</div>
+
+<div align="center">
+
+[![Install in Claude Desktop](https://img.shields.io/badge/Install_in-Claude_Desktop-D97757?style=for-the-badge&logo=anthropic&logoColor=white)](https://github.com/cyanheads/protein-mcp-server/releases/latest/download/protein-mcp-server.mcpb) [![Install in Cursor](https://cursor.com/deeplink/mcp-install-dark.svg)](https://cursor.com/en/install-mcp?name=protein-mcp-server&config=eyJjb21tYW5kIjoibnB4IiwiYXJncyI6WyIteSIsIkBjeWFuaGVhZHMvcHJvdGVpbi1tY3Atc2VydmVyIl19) [![Install in VS Code](https://img.shields.io/badge/VS_Code-Install_Server-0098FF?style=for-the-badge&logo=visualstudiocode&logoColor=white)](https://vscode.dev/redirect?url=vscode:mcp/install?%7B%22name%22%3A%22protein-mcp-server%22%2C%22command%22%3A%22npx%22%2C%22args%22%3A%5B%22-y%22%2C%22%40cyanheads%2Fprotein-mcp-server%22%5D%7D)
+
+[![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-67E8F9?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
+
+</div>
+
+---
+
+## Tools
+
+Seven tools spanning the structure-research arc — discover, fetch, find homologs, track ligands, compare, profile the corpus, and annotate — over experimental (PDB) and predicted (AlphaFold) structures from one surface:
+
+| Tool | Description |
+|:---|:---|
+| `protein_search_structures` | Search experimental and predicted structures by free text, sequence, or organism/method/resolution filters, with optional facet breakdowns. |
+| `protein_get_structure` | Fetch metadata and coordinate-file URLs by ID — experimental (PDB), predicted (AlphaFold), or best-available — with batch partial success and optional coordinate inlining. |
+| `protein_find_similar` | Find sequence homologs (RCSB mmseqs2) or fold homologs (Foldseek) from a sequence, PDB ID, or UniProt accession. |
+| `protein_track_ligands` | Resolve ligand names/formulas to component IDs, find structures containing a ligand, or map binding-site residues. |
+| `protein_compare_structures` | Structurally align 2–10 structures (TM-align / jFATCAT) to a reference or as a full pairwise matrix. |
+| `protein_analyze_collection` | Profile the PDB into distributions and trends with server-side facets — counts, histograms, timelines, and cross-tabs. |
+| `protein_get_annotations` | Fetch UniProt features and natural variants plus InterPro domain/family memberships with GO terms. |
+
+### `protein_search_structures`
+
+Federated search across experimental (PDB) and predicted (computed-model) structures via RCSB Search v2.
+
+- Free-text, protein-sequence (triggers an mmseqs2 similarity search), and organism / method / resolution filters
+- `content_type` scopes the search to `experimental`, `predicted`, or `all`
+- Experimental hits are enriched with title, method, resolution, and organism
+- Optional `facets` return a method / organism / release-year breakdown alongside the hits at no extra call
+- Chain hit IDs straight into `protein_get_structure`
+
+---
+
+### `protein_get_structure`
+
+Fetch structures with metadata and coordinate-file URLs, resolving across providers by `source`.
+
+- `source: experimental` takes PDB entry IDs, batched in one RCSB GraphQL call
+- `source: predicted` takes UniProt accessions and returns the AlphaFold model with pLDDT/PAE confidence
+- `source: best_available` takes UniProt accessions and returns the top federated model (experimental if one exists, else the best prediction)
+- Per-ID partial success — unresolved IDs are listed in `failed[]`, not a batch-level error
+- `include_coords` inlines coordinate content; when a batch overflows the response budget it returns a per-structure size outline, so you can re-call with `sections: [ids]` for specific structures
+
+---
+
+### `protein_find_similar`
+
+Find structurally or evolutionarily related proteins, by sequence or by fold.
+
+- `by: sequence` runs a synchronous RCSB mmseqs2 search; `by: structure` runs an asynchronous Foldseek search against experimental and predicted databases
+- Query from a raw one-letter sequence, a PDB ID, or a UniProt accession
+- Foldseek targets default to `pdb100` + `afdb50`; override via `databases` (e.g. `afdb-swissprot`, `BFVD`)
+- Async jobs that exceed the poll budget return `status: computing` with a ticket — re-call to resume
+- Each hit names the engine and source database it came from
+
+---
+
+### `protein_track_ligands`
+
+Ligand discovery and binding-site analysis across the PDB.
+
+- `mode: find_ligand` resolves a name or formula to chemical component IDs with formula, weight, SMILES, and InChIKey
+- `mode: structures_with_ligand` returns PDB entries containing a ligand by exact component ID
+- `mode: binding_site` returns the protein residues lining a ligand's pocket in a structure, with contact distances
+- Binding sites are experimental-only — computed from deposited coordinates (predicted models carry no bound ligands)
+
+---
+
+### `protein_compare_structures`
+
+Structural alignment of 2–10 structures via the RCSB Structural Comparison service.
+
+- Methods: `tm-align`, `fatcat-rigid`, `fatcat-flexible`
+- `reference: first` aligns every structure to the first; `reference: all_pairs` computes the full pairwise matrix
+- Optional per-structure `chain` restricts the alignment to a single chain
+- Each pair is an independent async job, fanned out with a concurrency cap and per-pair partial success — a pair still computing when the budget elapses returns `status: computing` with its job UUID, and a failed pair degrades its row without sinking the others
+- Returns TM-score, RMSD, and aligned-residue count per pair
+
+---
+
+### `protein_analyze_collection`
+
+Profile the PDB into distributions and trends over an optional scoping query — backed by RCSB's server-side facet engine (one call, compact buckets, no row pull).
+
+- Group by `method`, `organism`, `polymer_type`, `resolution`, `release_year`, or `molecular_weight`
+- One `group_by` dimension for a breakdown, or two for a cross-tab (the first nests the second)
+- `interval` sets the bin width for value histograms or the period for date histograms (`year` / `month` / `quarter`)
+- Scope with a free-text `query`, `organism`, `method`, or `max_resolution`; `content_type` selects the structure universe
+- `bucket_limit` caps buckets per dimension; truncation is flagged in the response
+
+---
+
+### `protein_get_annotations`
+
+Sequence and functional annotation for a protein.
+
+- UniProt features (domains, binding sites, PTMs) and natural sequence variants
+- InterPro domain/family memberships (Pfam, PROSITE, …) with associated GO terms
+- Provide a UniProt accession directly, or a PDB ID — resolved to its accession via the structure's sequence cross-reference
+- `include` scopes which annotation classes are fetched: `features`, `domains`, `variants`, or `all`
+
+## Resources
+
+| Type | Name | Description |
+|:---|:---|:---|
+| Resource | `pdb://{entry_id}` | Experimental structure summary for a PDB entry — title, method, resolution, organism, chains, and bound ligands. |
+| Resource | `af://{uniprot}` | Predicted-structure summary for a UniProt accession from AlphaFold DB — mean pLDDT, confidence-band fractions, model URLs, and version. |
+
+All resource data is also reachable via tools — `pdb://{entry_id}` mirrors `protein_get_structure` for `source: experimental`, and `af://{uniprot}` mirrors it for `source: predicted`. Many MCP clients are tool-only and don't surface resources; the summaries remain reachable through the tools.
+
+## Features
+
+Built on [`@cyanheads/mcp-ts-core`](https://www.npmjs.com/package/@cyanheads/mcp-ts-core):
+
+- Declarative tool and resource definitions — single file per primitive, framework handles registration and validation
+- Unified error handling — handlers throw, framework catches, classifies, and formats
+- Pluggable auth: `none`, `jwt`, `oauth`
+- Swappable storage backends: `in-memory`, `filesystem`, `Supabase`, `Cloudflare KV/R2/D1`
+- Structured logging with optional OpenTelemetry tracing
+- STDIO and Streamable HTTP transports
+
+Protein-specific:
+
+- One federated surface over experimental (PDB) and predicted (AlphaFold / 3D-Beacons) structures — search, fetch, and compare treat both universes the same
+- Keyless across every upstream — RCSB, AlphaFold DB, 3D-Beacons, UniProt, InterPro, and Foldseek, no API keys to provision
+- Corpus analytics run server-side on RCSB's facet engine — distributions, histograms, and cross-tabs in one call, no row pull and no SQL workspace
+- Async alignment and Foldseek jobs poll within a bounded budget and hand back a resumable ticket instead of blocking
+
+Agent-friendly output:
+
+- Provenance on every response — each hit carries a `source` (`experimental` / `predicted`), the engine and database that produced it, and effective-query / total-count echoes so agents can reason about coverage
+- Graceful partial failure — batch fetches and pairwise comparisons return per-item rows (`failed[]`, per-pair `status`) instead of failing the whole request, each with actionable recovery text
+- Discriminated output contracts — typed `source` and `status` unions, `computing` results with resume tickets, and budget-overflow outlines let callers branch on data, not string parsing
+
+## Getting started
+
+Add the following to your MCP client configuration file. No API key is required — every upstream provider is keyless.
+
+```json
+{
+  "mcpServers": {
+    "protein-mcp-server": {
+      "type": "stdio",
+      "command": "bunx",
+      "args": ["@cyanheads/protein-mcp-server@latest"],
+      "env": {
+        "MCP_TRANSPORT_TYPE": "stdio",
+        "MCP_LOG_LEVEL": "info"
+      }
+    }
+  }
+}
+```
+
+Or with npx (no Bun required):
+
+```json
+{
+  "mcpServers": {
+    "protein-mcp-server": {
+      "type": "stdio",
+      "command": "npx",
+      "args": ["-y", "@cyanheads/protein-mcp-server@latest"],
+      "env": {
+        "MCP_TRANSPORT_TYPE": "stdio",
+        "MCP_LOG_LEVEL": "info"
+      }
+    }
+  }
+}
+```
+
+Or with Docker:
+
+```json
+{
+  "mcpServers": {
+    "protein-mcp-server": {
+      "type": "stdio",
+      "command": "docker",
+      "args": ["run", "-i", "--rm", "-e", "MCP_TRANSPORT_TYPE=stdio", "ghcr.io/cyanheads/protein-mcp-server:latest"]
+    }
+  }
+}
+```
+
+For Streamable HTTP, set the transport and start the server:
+
+```sh
+MCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 bun run start:http
+# Server listens at http://localhost:3010/mcp
+```
+
+### Prerequisites
+
+- [Bun v1.3.2](https://bun.sh/) or higher (or Node.js v24+).
+- No accounts or API keys — RCSB, AlphaFold DB, 3D-Beacons, UniProt, InterPro, and Foldseek are all public and keyless.
+
+### Installation
+
+1. **Clone the repository:**
+
+```sh
+git clone https://github.com/cyanheads/protein-mcp-server.git
+```
+
+2. **Navigate into the directory:**
+
+```sh
+cd protein-mcp-server
+```
+
+3. **Install dependencies:**
+
+```sh
+bun install
+```
+
+## Configuration
+
+All upstream providers are keyless, so the server runs out of the box with no configuration. Every variable below is optional.
+
+| Variable | Description | Default |
+|:---|:---|:---|
+| `PROTEIN_ASYNC_POLL_TIMEOUT_MS` | Max wall-clock to poll an async job (alignment / Foldseek) before returning a `computing` result. | `30000` |
+| `PROTEIN_MAX_BATCH_IDS` | Cap on IDs accepted by `protein_get_structure` in one batch (1–100). | `25` |
+| `PROTEIN_MAX_COMPARE_STRUCTURES` | Cap on structures per `protein_compare_structures` call (2–25). | `10` |
+| `PROTEIN_FACET_BUCKET_CAP` | Default cap on buckets per `protein_analyze_collection` dimension (1–500). | `50` |
+| `PROTEIN_FANOUT_CONCURRENCY` | Max concurrent upstream requests for per-ID / per-pair fan-out (1–16). | `5` |
+| `RCSB_SEARCH_BASE_URL` | Base URL for the RCSB Search API v2. | `https://search.rcsb.org` |
+| `ALPHAFOLD_BASE_URL` | Base URL for the AlphaFold Protein Structure Database API. | `https://alphafold.ebi.ac.uk` |
+| `FOLDSEEK_BASE_URL` | Base URL for the Foldseek structural-similarity search service. | `https://search.foldseek.com` |
+| `MCP_TRANSPORT_TYPE` | Transport: `stdio` or `http`. | `stdio` |
+| `MCP_HTTP_PORT` | Port for the HTTP server. | `3010` |
+| `MCP_AUTH_MODE` | Auth mode: `none`, `jwt`, or `oauth`. | `none` |
+| `MCP_LOG_LEVEL` | Log level (RFC 5424). | `info` |
+| `OTEL_ENABLED` | Enable [OpenTelemetry instrumentation](https://github.com/cyanheads/mcp-ts-core/tree/main/docs/telemetry). | `false` |
+
+See [`.env.example`](./.env.example) for the full list of provider base-URL overrides and tuning limits.
+
+## Running the server
+
+### Local development
+
+- **Build and run:**
+
+  ```sh
+  # One-time build
+  bun run rebuild
+
+  # Run the built server
+  bun run start:stdio
+  # or
+  bun run start:http
+  ```
+
+- **Run checks and tests:**
+
+  ```sh
+  bun run devcheck   # Lint, format, typecheck, security
+  bun run test       # Vitest test suite
+  bun run lint:mcp   # Validate MCP definitions against spec
+  ```
+
+### Docker
+
+```sh
+docker build -t protein-mcp-server .
+docker run --rm -e MCP_TRANSPORT_TYPE=http -p 3010:3010 protein-mcp-server
+```
+
+The Dockerfile defaults to HTTP transport, stateless session mode, and logs to `/var/log/protein-mcp-server`. OpenTelemetry peer dependencies are installed by default — build with `--build-arg OTEL_ENABLED=false` to omit them.
+
+## Project structure
+
+| Directory | Purpose |
+|:---|:---|
+| `src/index.ts` | `createApp()` entry point — registers tools/resources and inits the provider services. |
+| `src/config` | Server-specific environment variable parsing and validation with Zod. |
+| `src/mcp-server/tools` | Tool definitions (`*.tool.ts`). |
+| `src/mcp-server/resources` | Resource definitions (`*.resource.ts`). |
+| `src/services` | Provider service layer — RCSB, AlphaFold, 3D-Beacons, UniProt, InterPro, Foldseek, and shared HTTP/identifier helpers. |
+| `tests/` | Unit and integration tests mirroring `src/`. |
+
+## Development guide
+
+See [`CLAUDE.md`/`AGENTS.md`](./CLAUDE.md) for development guidelines and architectural rules. The short version:
+
+- Handlers throw, framework catches — no `try/catch` in tool logic
+- Use `ctx.log` for request-scoped logging, `ctx.state` for tenant-scoped storage
+- Register new tools and resources via the barrels in `src/mcp-server/*/definitions/index.ts`
+- Wrap external API calls: validate raw → normalize to domain type → return output schema; never fabricate missing fields
+
+## Contributing
+
+Issues and pull requests are welcome. Run checks and tests before submitting:
+
+```sh
+bun run devcheck
+bun run test
+```
+
+## License
+
+Apache-2.0 — see [LICENSE](LICENSE) for details.

package/changelog/0.1.x/0.1.0.md

@@ -0,0 +1,21 @@
+---
+summary: "Initial release: federated protein structure & function across PDB, AlphaFold, UniProt, InterPro, and Foldseek — 7 tools, 2 resources."
+breaking: false
+security: false
+---
+
+# 0.1.0 — 2026-06-15
+
+Initial release. A Model Context Protocol server federating experimental (PDB) and predicted (AlphaFold) protein structures with sequence/functional annotation, ligand and binding-site analysis, structural search, and corpus-level faceting across the major public providers — all keyless.
+
+## Added
+
+- **`protein_search_structures`** — federated search over experimental (PDB) and predicted structures via RCSB Search v2: free-text, sequence (mmseqs2), and organism/method/resolution filters, with optional facet breakdowns and metadata-enriched hits.
+- **`protein_get_structure`** — batch fetch by ID across `experimental` / `predicted` / `best_available` sources, with per-ID partial success and optional coordinate inlining that degrades to a section outline on overflow.
+- **`protein_find_similar`** — sequence similarity (RCSB mmseqs2, synchronous) or fold similarity (Foldseek, async with ticket-resume) from a raw sequence, PDB ID, or UniProt accession.
+- **`protein_track_ligands`** — resolve ligand names/formulas to chemical component IDs, find structures containing a ligand, and analyze binding-site residues with contact distances.
+- **`protein_compare_structures`** — pairwise structural alignment of 2–10 structures (TM-align / jFATCAT) via the RCSB Structural Comparison service, concurrency-capped with per-pair partial success.
+- **`protein_analyze_collection`** — server-side PDB faceting: counts by method/organism/polymer type, resolution and molecular-weight histograms, release-year timelines, and two-dimensional cross-tabs.
+- **`protein_get_annotations`** — UniProt features (domains, binding sites, PTMs) and natural variants plus InterPro domain/family memberships with GO terms, by UniProt accession or resolved from a PDB ID.
+- **`pdb://{entry_id}`** and **`af://{uniprot}`** — injectable experimental and predicted structure-summary resources.
+- Optional environment configuration for every provider base URL plus tuning limits (batch size, comparison count, facet bucket cap, fan-out concurrency, async-poll timeout).

package/changelog/template.md

@@ -0,0 +1,127 @@
+---
+# FORMAT REFERENCE — do not edit. Copy this file to
+# `changelog/<major.minor>.x/<version>.md` (e.g. `changelog/0.8.x/0.8.6.md`)
+# to author a new release. Set that file's H1 to `# <version> — YYYY-MM-DD`
+# with a concrete date.
+
+# Required. One-line GitHub Release-style headline. 350 character cap.
+# Default short and scannable. Don't pad, don't stitch unrelated changes with
+# semicolons — pick the headline. Quotes required: unquoted YAML treats `: `
+# inside the value as a key separator and fails GitHub's strict parser.
+summary: ""
+
+# Set `true` when consumers must change code to upgrade: API removals,
+# signature changes, config renames, behavior changes that break existing
+# usage. Flagged as `Breaking` in the rollup.
+breaking: false
+
+# Set `true` if this release contains any security fix. Pairs with the
+# `## Security` section below. Flagged as `Security` in the rollup so
+# users can triage upgrade urgency at a glance.
+security: false
+
+# Optional free-form notes for maintenance agents processing this release.
+# Not rendered in CHANGELOG — consumed by agents running `maintenance` on
+# downstream servers. Use for adoption instructions that don't fit the
+# human-facing sections: new files to create, fields to populate, one-time
+# migration steps. Omit the field entirely when there's nothing to say.
+# agent-notes: |
+#   <instructions for downstream maintenance agents>
+---
+
+# <version> — YYYY-MM-DD
+
+<!--
+  AUTHORING GUIDE — applies to the new per-version file you create from this
+  template.
+
+  Audience: someone scanning release notes to decide what affects them. Lead
+  each bullet with the symbol or concept name in **bold** so they can skip
+  what's irrelevant and zoom in on what's not.
+
+  Tone: terse, fact-dense, not verbose. Default to one sentence per bullet —
+  name the symbol, state what changed, stop. Use a second sentence only when
+  it carries weight. If a bullet feels long, it is.
+
+  Cut: mechanism walkthroughs (those belong in JSDoc, CLAUDE.md/AGENTS.md, or the
+  relevant skill), ceremonial framings ("This release introduces…",
+  backwards-compat paragraphs), file-by-file test enumerations, internal
+  implementation notes. Prefer code/symbol names over English re-explanations.
+
+  Narrative intro: skip by default. Add one short sentence only when the
+  release theme genuinely needs framing the bullets can't carry.
+
+  Sections: Keep a Changelog order — Added, Changed, Deprecated, Removed,
+  Fixed, Security. Include only sections with entries; delete the rest
+  (including the commented-out scaffolding below). Don't ship empty headers.
+
+  Include: every distinct fact a reader needs to adopt or audit the release —
+  new exports, signatures, lint rule IDs, env vars, breaking changes, version
+  bumps on shipped skills. Nothing more.
+
+  Links: link issues, PRs, docs, or skills where they help a reader jump to
+  context. Once per item per entry — don't re-link the same issue in summary,
+  narrative, and bullet. Skip links for inline symbol names; code spans speak
+  for themselves.
+
+  Issue/PR URLs: use full URLs. GitHub's bare `#NN` auto-link only resolves
+  inside its own UI, not in npm reads or local editors.
+
+      [#38](https://github.com/cyanheads/mcp-ts-core/issues/38)   ← issue
+      [#42](https://github.com/cyanheads/mcp-ts-core/pull/42)     ← PR
+
+  Verify numbers exist before linking (`gh issue view NN`, `gh pr view NN`).
+  Never speculate on a future number — `#42` for an upcoming PR silently
+  resolves to whatever real item already owns 42, and timeline previews pull
+  in that unrelated item's metadata.
+
+  TAG ANNOTATIONS — the annotated tag body renders as the GitHub Release body
+  via `gh release create --notes-from-tag`. The tag is a derivative of this
+  changelog entry — a condensed, scannable version, not a copy. Format:
+
+    <theme — omit version number, GitHub prepends it>
+                                                          ← blank line
+    <1-2 sentence context: what this release does>
+                                                          ← blank line
+    Dependency bumps:                                     ← section header
+                                                          ← blank line
+    - `@cyanheads/mcp-ts-core` ^0.9.1 → ^0.9.6          ← bullet
+                                                          ← blank line
+    Changed:                                              ← only sections with entries
+                                                          ← blank line
+    - `format()` output includes `query` in text mode
+                                                          ← blank line
+    Added:
+                                                          ← blank line
+    - `manifest.json` scaffolded for MCPB bundle support
+    - Install badges (Claude Desktop, Cursor, VS Code)
+                                                          ← blank line
+    <N> tests pass; `bun run devcheck` clean.             ← footer
+
+  Never a flat comma-separated string. Always structured markdown with
+  sections. The tag must scan well as a rendered GitHub Release page.
+-->
+
+## Added
+
+-
+
+## Changed
+
+-
+
+<!-- ## Deprecated
+
+- -->
+
+<!-- ## Removed
+
+- -->
+
+## Fixed
+
+-
+
+<!-- ## Security
+
+- -->