@cyanheads/protein-mcp-server 0.1.3 → 0.2.0

package/AGENTS.md

@@ -1,8 +1,8 @@
 # Developer Protocol
 
 **Server:** protein-mcp-server
-**Version:** 0.1.3
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.9`
+**Version:** 0.2.0
+**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.10`
 **Engines:** Bun ≥1.3.0, Node ≥24.0.0
 **MCP SDK:** `@modelcontextprotocol/sdk` ^1.29.0
 **Zod:** ^4.4.3
@@ -171,7 +171,7 @@ await createApp({
   resources: [pdbSummaryResource, afSummaryResource],
   prompts: [],
   landing: { requireAuth: false }, // public, keyless data server
-  instructions: 'protein-mcp-server — federated protein structure & function over experimental (PDB) and predicted (AlphaFold) structures. No API keys required.',
+  instructions: 'protein-mcp-server — federated protein structure & annotation over experimental (PDB) and predicted (AlphaFold) structures.',
   setup(core) { /* init the six provider services */ },
 });
 ```

package/CLAUDE.md

@@ -1,8 +1,8 @@
 # Developer Protocol
 
 **Server:** protein-mcp-server
-**Version:** 0.1.3
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.9`
+**Version:** 0.2.0
+**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.10`
 **Engines:** Bun ≥1.3.0, Node ≥24.0.0
 **MCP SDK:** `@modelcontextprotocol/sdk` ^1.29.0
 **Zod:** ^4.4.3
@@ -171,7 +171,7 @@ await createApp({
   resources: [pdbSummaryResource, afSummaryResource],
   prompts: [],
   landing: { requireAuth: false }, // public, keyless data server
-  instructions: 'protein-mcp-server — federated protein structure & function over experimental (PDB) and predicted (AlphaFold) structures. No API keys required.',
+  instructions: 'protein-mcp-server — federated protein structure & annotation over experimental (PDB) and predicted (AlphaFold) structures.',
   setup(core) { /* init the six provider services */ },
 });
 ```

package/README.md

@@ -1,13 +1,13 @@
 <div align="center">
   <h1>@cyanheads/protein-mcp-server</h1>
-  <p><b>Federated protein structure & function across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.</b>
+  <p><b>Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.</b>
   <div>7 Tools • 2 Resources</div>
   </p>
 </div>
 
 <div align="center">
 
-[![Version](https://img.shields.io/badge/Version-0.1.3-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/)
+[![Version](https://img.shields.io/badge/Version-0.2.0-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>
 
@@ -37,7 +37,7 @@ Seven tools spanning the structure-research arc — discover, fetch, find homolo
 | `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_compare_structures` | Structurally align multiple 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. |
 
@@ -72,7 +72,7 @@ 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
+- Async jobs that exceed the poll budget return `status: computing` with a `ticketId` — re-call with `ticket_id` set to that value to poll the same job instead of resubmitting
 - Each hit names the engine and source database it came from
 
 ---
@@ -90,12 +90,13 @@ Ligand discovery and binding-site analysis across the PDB.
 
 ### `protein_compare_structures`
 
-Structural alignment of 2–10 structures via the RCSB Structural Comparison service.
+Structural alignment of multiple structures (up to the configured `PROTEIN_MAX_COMPARE_STRUCTURES` cap) 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
+- 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
+- Re-call with a matching `{ a, b, uuid }` entry in `resume[]` (copied from a prior response's `pairs[]`) to poll a computing pair's job instead of resubmitting
 - Returns TM-score, RMSD, and aligned-residue count per pair
 
 ---
@@ -146,7 +147,7 @@ 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
+- Async alignment and Foldseek jobs poll within a bounded budget and hand back a job ticket (`ticketId` / per-pair `uuid`) instead of blocking — re-call with `ticket_id` or a `resume[]` entry to poll the same job instead of resubmitting
 
 Agent-friendly output:
 

package/changelog/0.1.x/0.1.4.md

@@ -0,0 +1,15 @@
+---
+summary: "Narrow the public description and server instructions from 'structure & function' to 'structure & annotation'. No behavior changes."
+breaking: false
+security: false
+---
+
+# 0.1.4 — 2026-06-23
+
+Copy refinement. No tool, resource, schema, or behavior changes.
+
+## Changed
+
+- **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.
+- **`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.
+- **Dependencies** — `@biomejs/biome` (dev) 2.5.0 → 2.5.1.

package/changelog/0.2.x/0.2.0.md

@@ -0,0 +1,25 @@
+---
+summary: "Resume protein_find_similar and protein_compare_structures jobs by ticket/UUID instead of resubmitting; compare_structures structures cap widened to the configured 2–25 range with a truncation notice; dependency refresh clears a moderate js-yaml advisory."
+breaking: false
+security: true
+---
+
+# 0.2.0 — 2026-07-03
+
+## Added
+
+- **`protein_find_similar`** — new optional `ticket_id` input. When set on a `by:"structure"` call, polls the existing Foldseek job instead of resolving coordinates and submitting a new search; `pdb_id`/`uniprot`/`databases` are ignored. New error reason `ticket_not_found` when the ticket is invalid or expired. ([#8](https://github.com/cyanheads/protein-mcp-server/issues/8))
+- **`protein_compare_structures`** — new optional `resume` input: an array of `{ a, b, uuid }` entries copied from a prior response's `pairs[]`. A pair whose labels match a `resume` entry (order- and case-insensitive) polls the given UUID instead of submitting a fresh alignment job; unmatched pairs still submit fresh. New error reason `resume_pair_unmatched` when a `resume` entry's labels don't match any pair generated from `structures` + `reference`. ([#8](https://github.com/cyanheads/protein-mcp-server/issues/8))
+- **`AlignmentService.resumePair`** / **`FoldseekService.resume`** — service-level resume methods backing the two tools above. Both reuse the existing polling step and never throw; `resumePair` treats a `404` as `computing` (the RCSB alignment API returns the same 404 for an expired UUID and a job still in flight, so it can't safely report not-found), while `resume` distinguishes a Foldseek `400 "invalid ID"` as a genuine `not_found`.
+
+## Changed
+
+- **`protein_compare_structures`** — `structures` cap widened from a hardcoded `.max(10)` to `.max(25)`, matching the existing `PROTEIN_MAX_COMPARE_STRUCTURES` config ceiling (2–25, default 10). A request exceeding the configured cap now surfaces a truncation notice (previously silent). Tool and field descriptions reworded off the hardcoded "2–10" language to describe the configured cap. ([#11](https://github.com/cyanheads/protein-mcp-server/issues/11))
+- **Dependencies:**
+  - `@cyanheads/mcp-ts-core` ^0.10.9 → ^0.10.10
+  - `@biomejs/biome` 2.5.1 → 2.5.2 (dev)
+  - `@types/node` 26.0.0 → 26.1.0 (dev)
+
+## Security
+
+- **`js-yaml`** — the dependency refresh (`@cyanheads/mcp-ts-core` bump + lockfile re-resolve) moves the transitive `js-yaml` resolution from 3.14.2 to 3.15.0, clearing [GHSA-h67p-54hq-rp68](https://github.com/advisories/GHSA-h67p-54hq-rp68) (quadratic-complexity ReDoS in `js-yaml < 3.15.0`). `bun audit`: 1 moderate → 0.

package/dist/index.js

@@ -31,15 +31,7 @@ await createApp({
     prompts: [],
     // Public, keyless data server — serve the full inventory to unauthenticated callers.
     landing: { requireAuth: false },
-    instructions: 'protein-mcp-server — federated protein structure & function research over experimental (PDB) and ' +
-        'predicted (AlphaFold) structures. No API keys required.\n' +
-        '- protein_search_structures: find structures by text, sequence, or organism/method/resolution; optional facet breakdown\n' +
-        '- protein_get_structure: fetch metadata + coordinate URLs for PDB IDs or UniProt accessions (batch, partial success)\n' +
-        '- protein_find_similar: sequence (mmseqs2) or structure (Foldseek) similarity search\n' +
-        '- protein_track_ligands: resolve ligands, find structures containing them, or map binding-site residues\n' +
-        '- protein_compare_structures: pairwise TM-align / jFATCAT over 2–10 structures\n' +
-        '- protein_analyze_collection: server-side facet distributions and trends over the PDB\n' +
-        '- protein_get_annotations: UniProt features + InterPro domains/GO terms',
+    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).',
     setup(core) {
         const serverConfig = getServerConfig();
         initRcsbService(core.config, core.storage, serverConfig);

package/dist/index.js.map

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/compare-structures.tool.d.ts

@@ -6,6 +6,7 @@
  * @module mcp-server/tools/definitions/compare-structures.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 export declare const compareStructures: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
     structures: z.ZodArray<z.ZodObject<{
         pdb_id: z.ZodString;
@@ -21,6 +22,11 @@ export declare const compareStructures: import("@cyanheads/mcp-ts-core").ToolDef
         "fatcat-flexible": "fatcat-flexible";
     }>>;
     timeout_s: z.ZodOptional<z.ZodNumber>;
+    resume: z.ZodOptional<z.ZodArray<z.ZodObject<{
+        a: z.ZodString;
+        b: z.ZodString;
+        uuid: z.ZodString;
+    }, z.core.$strip>>>;
 }, z.core.$strip>, z.ZodObject<{
     method: z.ZodString;
     reference: z.ZodEnum<{
@@ -41,7 +47,12 @@ export declare const compareStructures: import("@cyanheads/mcp-ts-core").ToolDef
         uuid: z.ZodOptional<z.ZodString>;
         error: z.ZodOptional<z.ZodString>;
     }, z.core.$strip>>;
-}, z.core.$strip>, undefined, {
+}, z.core.$strip>, readonly [{
+    readonly reason: "resume_pair_unmatched";
+    readonly code: JsonRpcErrorCode.InvalidParams;
+    readonly when: "A resume entry's a/b labels don't match any pair generated from structures + reference.";
+    readonly recovery: "Copy each resume entry's a, b, and uuid verbatim from a prior response's pairs[], and keep structures and reference unchanged between calls.";
+}], {
     readonly pairsTotal: z.ZodNumber;
     readonly computing: z.ZodNumber;
     readonly notice: z.ZodOptional<z.ZodString>;

package/dist/mcp-server/tools/definitions/compare-structures.tool.d.ts.map

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/compare-structures.tool.js

@@ -6,6 +6,7 @@
  * @module mcp-server/tools/definitions/compare-structures.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { getServerConfig } from '../../../config/server-config.js';
 import { getAlignmentService } from '../../../services/alignment/alignment-service.js';
 import { mapWithConcurrency } from '../../../services/shared/async.js';
@@ -21,8 +22,8 @@ const inputSchema = z.object({
     })
         .describe('A structure to align, by PDB entry ID with optional chain.'))
         .min(2)
-        .max(10)
-        .describe('The 2–10 structures to compare.'),
+        .max(25)
+        .describe('The structures to compare, up to the configured batch cap (excess is dropped with a notice).'),
     reference: z
         .enum(['first', 'all_pairs'])
         .default('first')
@@ -38,6 +39,25 @@ const inputSchema = z.object({
         .max(120)
         .optional()
         .describe('Poll budget per pair in seconds before returning "computing". Defaults to the server setting.'),
+    resume: z
+        .array(z
+        .object({
+        a: z
+            .string()
+            .min(1)
+            .describe('First structure label (entry or entry.chain) of a pair from a prior response.'),
+        b: z
+            .string()
+            .min(1)
+            .describe('Second structure label (entry or entry.chain) of a pair from a prior response.'),
+        uuid: z
+            .string()
+            .min(1)
+            .describe('Alignment job UUID returned for that pair by a prior call.'),
+    })
+        .describe('A prior pair to resume by UUID instead of resubmitting.'))
+        .optional()
+        .describe("Resume tickets from a prior call: for each pair whose labels match an entry here, poll the existing UUID instead of submitting a new alignment job. Copy a, b, and uuid verbatim from a prior response's pairs[]; keep structures and reference unchanged."),
 });
 const outputSchema = z.object({
     method: z.string().describe('Alignment method used.'),
@@ -62,13 +82,22 @@ const outputSchema = z.object({
 });
 export const compareStructures = tool('protein_compare_structures', {
     title: 'protein-mcp-server: compare structures',
-    description: 'Structurally align 2–10 structures via the RCSB Structural Comparison service (TM-align / jFATCAT). ' +
-        'reference:"first" aligns every structure to the first; reference:"all_pairs" computes the full pairwise ' +
-        'matrix. Each pair is an independent async alignment 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 (re-call to resume), and a failed pair degrades its row without sinking the others. Returns ' +
-        'TM-score, RMSD, and aligned-residue count per pair.',
+    description: 'Structurally align multiple structures (up to the configured batch cap) via the RCSB Structural ' +
+        'Comparison service (TM-align / jFATCAT). reference:"first" aligns every structure to the first; ' +
+        'reference:"all_pairs" computes the full pairwise matrix. Each pair is an independent async alignment ' +
+        '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. Re-call with a matching entry in resume[] to poll a computing pair's UUID instead " +
+        'of resubmitting. Returns TM-score, RMSD, and aligned-residue count per pair.',
     annotations: { readOnlyHint: true, openWorldHint: true },
+    errors: [
+        {
+            reason: 'resume_pair_unmatched',
+            code: JsonRpcErrorCode.InvalidParams,
+            when: "A resume entry's a/b labels don't match any pair generated from structures + reference.",
+            recovery: "Copy each resume entry's a, b, and uuid verbatim from a prior response's pairs[], and keep structures and reference unchanged between calls.",
+        },
+    ],
     input: inputSchema,
     output: outputSchema,
     enrichment: {
@@ -79,12 +108,33 @@ export const compareStructures = tool('protein_compare_structures', {
     async handler(input, ctx) {
         const cfg = getServerConfig();
         const structures = input.structures.slice(0, cfg.maxCompareStructures);
+        const notices = [];
+        if (input.structures.length > cfg.maxCompareStructures) {
+            notices.push(`Capped at ${cfg.maxCompareStructures} structures; ${input.structures.length - cfg.maxCompareStructures} ignored.`);
+        }
         const timeoutMs = input.timeout_s ? input.timeout_s * 1000 : cfg.asyncPollTimeoutMs;
         const method = input.method;
         const pairs = buildPairs(structures, input.reference);
+        // Map each supplied resume ticket to a pair. A ticket that matches no pair in
+        // the current structures/reference set is a client error — fail loudly rather
+        // than silently resubmit and burn a fresh alignment job.
+        const resumeByPair = new Map();
+        if (input.resume?.length) {
+            const validKeys = new Set(pairs.map(([a, b]) => pairKey(label(a), label(b))));
+            for (const r of input.resume) {
+                const key = pairKey(r.a, r.b);
+                if (!validKeys.has(key)) {
+                    throw ctx.fail('resume_pair_unmatched', `Resume entry ${r.a} ↔ ${r.b} matches no pair in the current structures/reference set.`, { ...ctx.recoveryFor('resume_pair_unmatched') });
+                }
+                resumeByPair.set(key, r.uuid);
+            }
+        }
         const alignment = getAlignmentService();
         const rows = await mapWithConcurrency(pairs, cfg.fanoutConcurrency, async ([a, b]) => {
-            const outcome = await alignment.comparePair(toCompare(a), toCompare(b), method, timeoutMs, ctx);
+            const resumeUuid = resumeByPair.get(pairKey(label(a), label(b)));
+            const outcome = resumeUuid
+                ? await alignment.resumePair(resumeUuid, timeoutMs, ctx)
+                : await alignment.comparePair(toCompare(a), toCompare(b), method, timeoutMs, ctx);
             const base = { a: label(a), b: label(b) };
             if (outcome.status === 'complete') {
                 return {
@@ -109,9 +159,11 @@ export const compareStructures = tool('protein_compare_structures', {
         const failed = rows.filter((r) => r.status === 'failed').length;
         ctx.enrich({ pairsTotal: rows.length, computing });
         if (computing > 0 || failed > 0) {
-            ctx.enrich.notice(`${computing} pair(s) still computing${failed > 0 ? `, ${failed} failed` : ''}. ` +
-                `Re-call to resume computing pairs (cold alignment jobs typically finish within 30–60 s).`);
+            notices.push(`${computing} pair(s) still computing${failed > 0 ? `, ${failed} failed` : ''}. ` +
+                `Re-call with a resume entry per pair (copy a, b, uuid from the pairs above) to poll existing jobs — cold alignment jobs typically finish within 30–60 s.`);
         }
+        if (notices.length > 0)
+            ctx.enrich.notice(notices.join(' '));
         return { method, reference: input.reference, pairs: rows };
     },
     format: (result) => {
@@ -165,4 +217,11 @@ function toCompare(s) {
 function label(s) {
     return s.chain ? `${s.pdb_id.toUpperCase()}.${s.chain}` : s.pdb_id.toUpperCase();
 }
+/**
+ * Canonical, order- and case-insensitive key for a pair of structure labels, so a
+ * resume entry matches its pair regardless of which side the client copied first.
+ */
+function pairKey(a, b) {
+    return [a.toUpperCase(), b.toUpperCase()].sort().join('');
+}
 //# sourceMappingURL=compare-structures.tool.js.map

package/dist/mcp-server/tools/definitions/compare-structures.tool.js.map

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package/dist/mcp-server/tools/definitions/find-similar.tool.d.ts

@@ -15,6 +15,7 @@ export declare const findSimilar: import("@cyanheads/mcp-ts-core").ToolDefinitio
     sequence: z.ZodOptional<z.ZodString>;
     pdb_id: z.ZodOptional<z.ZodString>;
     uniprot: z.ZodOptional<z.ZodString>;
+    ticket_id: z.ZodOptional<z.ZodString>;
     databases: z.ZodOptional<z.ZodArray<z.ZodString>>;
     max_evalue: z.ZodOptional<z.ZodNumber>;
     min_identity: z.ZodOptional<z.ZodNumber>;
@@ -60,6 +61,11 @@ export declare const findSimilar: import("@cyanheads/mcp-ts-core").ToolDefinitio
     readonly when: "The Foldseek search service rejected or failed the structure job.";
     readonly retryable: true;
     readonly recovery: "Retry shortly; if it persists, verify the source structure has coordinates via protein_get_structure.";
+}, {
+    readonly reason: "ticket_not_found";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "The supplied ticket_id was rejected by Foldseek as an invalid or expired ticket.";
+    readonly recovery: "Tickets expire once results age out; drop ticket_id and re-run the by:structure search from pdb_id or uniprot to get a fresh one.";
 }], {
     totalCount: z.ZodOptional<z.ZodNumber>;
     notice: z.ZodOptional<z.ZodString>;

package/dist/mcp-server/tools/definitions/find-similar.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"find-similar.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-similar.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAA6B,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACtE,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAkGjE,eAAO,MAAM,WAAW;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA+DtB,CAAC"}
+{"version":3,"file":"find-similar.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-similar.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAA6B,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACtE,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAwGjE,eAAO,MAAM,WAAW;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAuEtB,CAAC"}

package/dist/mcp-server/tools/definitions/find-similar.tool.js

@@ -26,6 +26,10 @@ const inputSchema = z.object({
         .describe('One-letter amino-acid sequence to search from (by:sequence).'),
     pdb_id: z.string().optional().describe('PDB entry ID to derive the query from.'),
     uniprot: z.string().optional().describe('UniProt accession to derive the query from.'),
+    ticket_id: z
+        .string()
+        .optional()
+        .describe('Foldseek ticket ID from a prior by:structure response whose status was "computing". When set, polls that existing job instead of submitting a new search (by:structure only) — pdb_id/uniprot/databases are ignored.'),
     databases: z
         .array(z.string())
         .optional()
@@ -48,7 +52,7 @@ const outputSchema = z.object({
     engine: z.string().describe('The engine that answered (e.g. "RCSB mmseqs2", "Foldseek").'),
     status: z
         .enum(['complete', 'computing'])
-        .describe('complete with hits, or computing (async, re-call to resume).'),
+        .describe('complete with hits, or computing (async — re-call with ticket_id to resume).'),
     ticketId: z
         .string()
         .optional()
@@ -93,8 +97,8 @@ export const findSimilar = tool('protein_find_similar', {
         'sequence-similarity search (synchronous) over a sequence — supplied directly, or pulled from a PDB ID ' +
         'or UniProt accession. by:"structure" runs a Foldseek fold-similarity search (asynchronous) against ' +
         'experimental and predicted databases; if the job is still computing when the poll budget elapses, the ' +
-        'response reports status "computing" with a ticket — re-call to resume. Output names the engine and ' +
-        'database each hit came from.',
+        'response reports status "computing" with a ticket — re-call with ticket_id set to that value to resume ' +
+        'the same job instead of resubmitting. Output names the engine and database each hit came from.',
     annotations: { readOnlyHint: true, openWorldHint: true },
     errors: [
         {
@@ -116,6 +120,12 @@ export const findSimilar = tool('protein_find_similar', {
             retryable: true,
             recovery: 'Retry shortly; if it persists, verify the source structure has coordinates via protein_get_structure.',
         },
+        {
+            reason: 'ticket_not_found',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'The supplied ticket_id was rejected by Foldseek as an invalid or expired ticket.',
+            recovery: 'Tickets expire once results age out; drop ticket_id and re-run the by:structure search from pdb_id or uniprot to get a fresh one.',
+        },
     ],
     input: inputSchema,
     output: outputSchema,
@@ -129,7 +139,7 @@ export const findSimilar = tool('protein_find_similar', {
     format: (result) => {
         const lines = [`## ${result.engine} (by:${result.by}) — ${result.status}`];
         if (result.ticketId)
-            lines.push(`**Ticket:** ${result.ticketId} — re-call to resume.`);
+            lines.push(`**Ticket:** ${result.ticketId} — re-call with ticket_id to resume.`);
         for (const h of result.hits) {
             lines.push(`\n### ${h.id} _(${h.source})_`);
             if (h.title)
@@ -182,15 +192,26 @@ async function runSequence(input, enrichLimit, ctx) {
     };
 }
 async function runStructure(input, timeoutMs, ctx) {
-    const { content, fileName } = await resolveCoordinateFile(input, ctx);
-    const outcome = await getFoldseekService().search({
-        fileContent: content,
-        fileName,
-        databases: input.databases && input.databases.length > 0 ? input.databases : DEFAULT_FOLDSEEK_DBS,
-        mode: FOLDSEEK_MODE,
-        limit: input.limit,
-        timeoutMs,
-    }, ctx);
+    const foldseek = getFoldseekService();
+    let outcome;
+    if (input.ticket_id) {
+        // Resume path: poll the existing ticket, skipping coordinate resolution + submit.
+        outcome = await foldseek.resume({ ticketId: input.ticket_id, limit: input.limit, timeoutMs }, ctx);
+    }
+    else {
+        const { content, fileName } = await resolveCoordinateFile(input, ctx);
+        outcome = await foldseek.search({
+            fileContent: content,
+            fileName,
+            databases: input.databases && input.databases.length > 0 ? input.databases : DEFAULT_FOLDSEEK_DBS,
+            mode: FOLDSEEK_MODE,
+            limit: input.limit,
+            timeoutMs,
+        }, ctx);
+    }
+    if (outcome.status === 'not_found') {
+        throw ctx.fail('ticket_not_found', `Foldseek ticket ${outcome.ticketId} is invalid or expired.`, { ...ctx.recoveryFor('ticket_not_found') });
+    }
     if (outcome.status === 'failed') {
         throw ctx.fail('search_failed', `Foldseek search failed: ${outcome.error}`, {
             recovery: {
@@ -199,7 +220,7 @@ async function runStructure(input, timeoutMs, ctx) {
         });
     }
     if (outcome.status === 'computing') {
-        ctx.enrich.notice(`Foldseek job still computing (ticket ${outcome.ticketId}). Re-call protein_find_similar to resume.`);
+        ctx.enrich.notice(`Foldseek job still computing (ticket ${outcome.ticketId}). Re-call protein_find_similar with ticket_id set to "${outcome.ticketId}" to resume.`);
         return {
             by: 'structure',
             engine: 'Foldseek',

package/dist/mcp-server/tools/definitions/find-similar.tool.js.map

@@ -1 +1 @@
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package/dist/services/alignment/alignment-service.d.ts

@@ -48,6 +48,14 @@ export declare class AlignmentService {
      * one bad pair doesn't sink the whole comparison.
      */
     comparePair(a: CompareStructure, b: CompareStructure, method: AlignmentMethod, timeoutMs: number, ctx: Context): Promise<PairOutcome>;
+    /**
+     * Resume an existing job: bounded-poll a UUID returned by a prior `comparePair`
+     * without resubmitting. Reuses the same `pollResult` step, so a `404` — which the
+     * RCSB API returns identically for an expired UUID and a job still computing —
+     * degrades to `{ status: 'computing' }` on timeout rather than a false `failed`.
+     * A legitimately in-flight job is never mistaken for a dead one. Never throws.
+     */
+    resumePair(uuid: string, timeoutMs: number, ctx: Context): Promise<PairOutcome>;
     /** Single poll of a job's results. 404 = still computing; a result body = ready. */
     private pollResult;
 }

package/dist/services/alignment/alignment-service.d.ts.map

@@ -1 +1 @@
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package/dist/services/alignment/alignment-service.js

@@ -66,6 +66,30 @@ export class AlignmentService {
             return { status: 'failed', error: err instanceof Error ? err.message : String(err) };
         }
     }
+    /**
+     * Resume an existing job: bounded-poll a UUID returned by a prior `comparePair`
+     * without resubmitting. Reuses the same `pollResult` step, so a `404` — which the
+     * RCSB API returns identically for an expired UUID and a job still computing —
+     * degrades to `{ status: 'computing' }` on timeout rather than a false `failed`.
+     * A legitimately in-flight job is never mistaken for a dead one. Never throws.
+     */
+    async resumePair(uuid, timeoutMs, ctx) {
+        try {
+            const outcome = await withAsyncPoll({
+                step: () => this.pollResult(uuid, ctx),
+                timeoutMs,
+                ctx,
+                intervalMs: 1500,
+                maxIntervalMs: 2500,
+            });
+            return outcome.status === 'complete'
+                ? { status: 'complete', uuid, scores: outcome.value }
+                : { status: 'computing', uuid };
+        }
+        catch (err) {
+            return { status: 'failed', error: err instanceof Error ? err.message : String(err) };
+        }
+    }
     /** Single poll of a job's results. 404 = still computing; a result body = ready. */
     async pollResult(uuid, ctx) {
         const res = await fetchResponse(`${this.resultsUrl}?uuid=${encodeURIComponent(uuid)}`, ctx, {

package/dist/services/alignment/alignment-service.js.map

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package/dist/services/foldseek/foldseek-service.d.ts

@@ -35,7 +35,7 @@ export interface FoldseekHit {
     /** UniProt accession (AlphaFold targets). */
     uniprotAccession?: string;
 }
-/** Outcome of a structural search. */
+/** Outcome of a structural search or ticket resume. */
 export type FoldseekOutcome = {
     status: 'complete';
     ticketId: string;
@@ -43,6 +43,9 @@ export type FoldseekOutcome = {
 } | {
     status: 'computing';
     ticketId: string;
+} | {
+    status: 'not_found';
+    ticketId: string;
 } | {
     status: 'failed';
     error: string;
@@ -62,6 +65,17 @@ export declare class FoldseekService {
         limit: number;
         timeoutMs: number;
     }, ctx: Context): Promise<FoldseekOutcome>;
+    /**
+     * Resume an existing ticket: bounded-poll a ticket returned by a prior `search`
+     * without resubmitting. A bogus or expired ticket is a clean `400 "invalid ID"`
+     * from Foldseek — surfaced as `{ status: 'not_found' }`, distinct from an
+     * in-flight job (`computing`) or a processing error (`failed`). Never throws.
+     */
+    resume(params: {
+        ticketId: string;
+        limit: number;
+        timeoutMs: number;
+    }, ctx: Context): Promise<FoldseekOutcome>;
     private submit;
     private pollTicket;
     private fetchResults;

package/dist/services/foldseek/foldseek-service.d.ts.map

@@ -1 +1 @@
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package/dist/services/foldseek/foldseek-service.js

@@ -6,6 +6,7 @@
  * Async: the ticket status field drives completion, not the HTTP code.
  * @module services/foldseek/foldseek-service
  */
+import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
 import { withAsyncPoll } from '../shared/async.js';
 import { fetchJson } from '../shared/http.js';
 export class FoldseekService {
@@ -41,6 +42,35 @@ export class FoldseekService {
             return { status: 'failed', error: err instanceof Error ? err.message : String(err) };
         }
     }
+    /**
+     * Resume an existing ticket: bounded-poll a ticket returned by a prior `search`
+     * without resubmitting. A bogus or expired ticket is a clean `400 "invalid ID"`
+     * from Foldseek — surfaced as `{ status: 'not_found' }`, distinct from an
+     * in-flight job (`computing`) or a processing error (`failed`). Never throws.
+     */
+    async resume(params, ctx) {
+        try {
+            const outcome = await withAsyncPoll({
+                step: () => this.pollTicket(params.ticketId, params.limit, ctx),
+                timeoutMs: params.timeoutMs,
+                ctx,
+                intervalMs: 1500,
+                maxIntervalMs: 2500,
+            });
+            return outcome.status === 'complete'
+                ? { status: 'complete', ticketId: params.ticketId, hits: outcome.value }
+                : { status: 'computing', ticketId: params.ticketId };
+        }
+        catch (err) {
+            // A 400 from the ticket/result endpoint is Foldseek's "invalid ID" — the
+            // ticket never existed or has expired. `fetchWithTimeout` maps 400 →
+            // InvalidParams, so key the not-found branch off that code.
+            if (err instanceof McpError && err.code === JsonRpcErrorCode.InvalidParams) {
+                return { status: 'not_found', ticketId: params.ticketId };
+            }
+            return { status: 'failed', error: err instanceof Error ? err.message : String(err) };
+        }
+    }
     async submit(fileContent, fileName, databases, mode, ctx) {
         const form = new FormData();
         form.append('q', new Blob([fileContent], { type: 'chemical/x-pdb' }), fileName);

package/dist/services/foldseek/foldseek-service.js.map

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package/package.json

@@ -1,8 +1,8 @@
 {
   "name": "@cyanheads/protein-mcp-server",
-  "version": "0.1.3",
+  "version": "0.2.0",
   "mcpName": "io.github.cyanheads/protein-mcp-server",
-  "description": "Federated protein structure & function across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.",
+  "description": "Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.",
   "type": "module",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
@@ -91,13 +91,13 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.10.9",
+    "@cyanheads/mcp-ts-core": "^0.10.10",
     "pino-pretty": "^13.1.3",
     "zod": "^4.4.3"
   },
   "devDependencies": {
-    "@biomejs/biome": "2.5.0",
-    "@types/node": "26.0.0",
+    "@biomejs/biome": "2.5.2",
+    "@types/node": "26.1.0",
     "depcheck": "^1.4.7",
     "ignore": "^7.0.5",
     "tsc-alias": "^1.8.17",

package/server.json

@@ -1,12 +1,12 @@
 {
   "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
   "name": "io.github.cyanheads/protein-mcp-server",
-  "description": "Federated protein structure & function across experimental (PDB) and predicted (AlphaFold) models.",
+  "description": "Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models.",
   "repository": {
     "url": "https://github.com/cyanheads/protein-mcp-server",
     "source": "github"
   },
-  "version": "0.1.3",
+  "version": "0.2.0",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.1.3",
+      "version": "0.2.0",
       "packageArguments": [
         {
           "type": "positional",
@@ -48,7 +48,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.1.3",
+      "version": "0.2.0",
       "packageArguments": [
         {
           "type": "positional",