npm - @cyanheads/protein-mcp-server - Versions diffs - 0.5.2 → 0.5.3 - Mend

@cyanheads/protein-mcp-server 0.5.2 → 0.5.3

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.

Files changed (22) hide show

package/AGENTS.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Developer Protocol
 **Server:** protein-mcp-server
-**Version:** 0.5.2
+**Version:** 0.5.3
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.12.3`
 **Engines:** Bun ≥1.3.0, Node ≥24.0.0
 **MCP SDK:** `@modelcontextprotocol/server` ^2.0.0

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Developer Protocol
 **Server:** protein-mcp-server
-**Version:** 0.5.2
+**Version:** 0.5.3
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.12.3`
 **Engines:** Bun ≥1.3.0, Node ≥24.0.0
 **MCP SDK:** `@modelcontextprotocol/server` ^2.0.0

package/README.md CHANGED Viewed

@@ -7,7 +7,7 @@
 <div align="center">
-[![Version](https://img.shields.io/badge/Version-0.5.2-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-^2.0.0-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-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.4.0-blueviolet.svg?style=flat-square)](https://bun.sh/)
+[![Version](https://img.shields.io/badge/Version-0.5.3-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-^2.0.0-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-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.4.0-blueviolet.svg?style=flat-square)](https://bun.sh/)
 </div>
@@ -47,7 +47,8 @@ Federated search across experimental (PDB) and predicted (computed-model) struct
 - Free-text, protein-sequence (triggers an mmseqs2 similarity search), and organism / method / resolution filters
 - `content_type` scopes the search to `experimental`, `predicted`, or `all` — the default `all` is a genuine union of both universes, so computed models appear alongside PDB entries
-- Every hit names its `source`; experimental hits are enriched with title, method, resolution, and organism, while computed models carry the UniProt accession parsed from their ID
+- Every hit names its `source`; experimental sequence hits expose a chainable PDB entry `id` plus the matched polymer `entityId`, with title, method, resolution, and organism enrichment, while computed models retain their complete model ID and parsed UniProt accession
+- `start` and `limit` page through ranked results; `nextStart` is returned while another page remains
 - Optional `facets` return a method / organism / release-year breakdown alongside the hits at no extra call, each reporting how many matches carry no value for that dimension; each dimension may be listed once
 - Chain hit IDs straight into `protein_get_structure`
@@ -72,6 +73,7 @@ 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
+- Sequence searches accept `start` with `limit` and return `nextStart` while another page remains
 - 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 `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
@@ -84,9 +86,12 @@ 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: structures_with_ligand` accepts `start` with `limit` and returns `nextStart` while another page remains
 - `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)
+Paged RCSB results preserve the upstream order within each response. Resolution ties and changes in the live corpus mean traversal is best-effort across calls, not a stable export snapshot.
 ---
 ### `protein_compare_structures`

package/changelog/0.5.x/0.5.3.md ADDED Viewed

@@ -0,0 +1,20 @@
+---
+summary: "RCSB-backed tools support offset pagination; structure searches accept method or resolution criteria alone, retain chainable sequence-hit IDs, and enrich every entry on a returned sequence page."
+breaking: false
+security: false
+---
+# 0.5.3 — 2026-08-30
+## Added
+- **RCSB result pagination**: `protein_search_structures`, sequence-mode `protein_find_similar`, and `structures_with_ligand` mode in `protein_track_ligands` accept `start` and return `nextStart` while more results remain ([#41](https://github.com/cyanheads/protein-mcp-server/issues/41)).
+## Changed
+- **Experimental sequence hits**: `protein_search_structures` exposes the chainable PDB entry as `id` and retains the matched polymer entity as `entityId` ([#39](https://github.com/cyanheads/protein-mcp-server/issues/39)).
+- **Filter-only structure searches**: experimental `method` and `max_resolution` now form valid RCSB search criteria without text, sequence, or organism input ([#40](https://github.com/cyanheads/protein-mcp-server/issues/40)).
+## Fixed
+- **Sequence-result enrichment**: `protein_find_similar` enriches every distinct entry returned on a sequence page instead of limiting metadata by the facet bucket cap ([#44](https://github.com/cyanheads/protein-mcp-server/issues/44)).

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

@@ -20,6 +20,7 @@ export declare const findSimilar: import("@cyanheads/mcp-ts-core").ToolDefinitio
     max_evalue: z.ZodOptional<z.ZodNumber>;
     min_identity: z.ZodOptional<z.ZodNumber>;
     limit: z.ZodDefault<z.ZodNumber>;
+    start: z.ZodDefault<z.ZodNumber>;
 }, z.core.$strip>, z.ZodObject<{
     by: z.ZodEnum<{
         sequence: "sequence";
@@ -69,6 +70,8 @@ export declare const findSimilar: import("@cyanheads/mcp-ts-core").ToolDefinitio
     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>;
+    start: z.ZodOptional<z.ZodNumber>;
+    nextStart: z.ZodOptional<z.ZodNumber>;
     notice: z.ZodOptional<z.ZodString>;
 }>;
 //# sourceMappingURL=find-similar.tool.d.ts.map

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

	@@ -1 +1 @@
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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;AA6HjE,eAAO,MAAM,WAAW;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwEtB,CAAC"}

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

@@ -46,6 +46,12 @@ const inputSchema = z.object({
         .optional()
         .describe('Minimum sequence identity 0–1 (by:sequence). Default 0.'),
     limit: z.number().int().min(1).max(100).default(25).describe('Maximum hits to return (1–100).'),
+    start: z
+        .number()
+        .int()
+        .min(0)
+        .default(0)
+        .describe('Zero-based result offset (by:sequence only).'),
 });
 const outputSchema = z.object({
     by: z.enum(['sequence', 'structure']).describe('Echoed similarity axis.'),
@@ -95,6 +101,11 @@ const enrichmentShape = {
         .number()
         .optional()
         .describe('Total upstream matches before pagination (by:sequence).'),
+    start: z.number().optional().describe('Zero-based offset of the sequence-result page.'),
+    nextStart: z
+        .number()
+        .optional()
+        .describe('Offset for the next sequence-result page; absent on the final or past-end page.'),
     notice: z.string().optional().describe('Advisory note (still computing, empty results).'),
 };
 export const findSimilar = tool('protein_find_similar', {
@@ -139,7 +150,7 @@ export const findSimilar = tool('protein_find_similar', {
     handler(input, ctx) {
         const cfg = getServerConfig();
         if (input.by === 'sequence')
-            return runSequence(input, cfg.facetBucketCap, ctx);
+            return runSequence(input, ctx);
         return runStructure(input, cfg.asyncPollTimeoutMs, ctx);
     },
     format: (result) => {
@@ -165,21 +176,27 @@ export const findSimilar = tool('protein_find_similar', {
         return [{ type: 'text', text: lines.join('\n') }];
     },
 });
-async function runSequence(input, enrichLimit, ctx) {
+async function runSequence(input, ctx) {
     const rcsb = getRcsbService();
     const sequence = await resolveSequence(input, ctx);
     const result = await rcsb.searchSequence(sequence, {
         ...(typeof input.max_evalue === 'number' ? { maxEvalue: input.max_evalue } : {}),
         ...(typeof input.min_identity === 'number' ? { minIdentity: input.min_identity } : {}),
         limit: input.limit,
+        start: input.start,
     }, ctx);
-    const entryIds = [...new Set(result.hits.map((h) => entryIdOf(h.id)))].slice(0, enrichLimit);
+    const entryIds = [...new Set(result.hits.map((h) => entryIdOf(h.id)))];
     const metaById = new Map();
     if (entryIds.length > 0) {
         for (const meta of await rcsb.getEntries(entryIds, ctx))
             metaById.set(meta.id, meta);
     }
     ctx.enrich.total(result.total);
+    const nextStart = input.start + result.hits.length;
+    ctx.enrich({
+        start: input.start,
+        ...(nextStart < result.total ? { nextStart } : {}),
+    });
     if (result.hits.length === 0)
         ctx.enrich.notice('No sequence-similar entries found. Lower min_identity or raise max_evalue.');
     return {

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package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts CHANGED Viewed

@@ -29,9 +29,11 @@ export declare const searchStructures: import("@cyanheads/mcp-ts-core").ToolDefi
         resolution: "resolution";
     }>>>;
     limit: z.ZodDefault<z.ZodNumber>;
+    start: z.ZodDefault<z.ZodNumber>;
 }, z.core.$strip>, z.ZodObject<{
     hits: z.ZodArray<z.ZodObject<{
         id: z.ZodString;
+        entityId: z.ZodOptional<z.ZodString>;
         source: z.ZodEnum<{
             experimental: "experimental";
             predicted: "predicted";
@@ -57,8 +59,8 @@ export declare const searchStructures: import("@cyanheads/mcp-ts-core").ToolDefi
 }, z.core.$strip>, readonly [{
     readonly reason: "no_criteria";
     readonly code: JsonRpcErrorCode.InvalidParams;
-    readonly when: "No query, sequence, or organism was provided — nothing to search on.";
-    readonly recovery: "Provide a free-text query, a protein sequence, or an organism name (filters alone are not enough).";
+    readonly when: "No query, sequence, organism, method, or maximum resolution was provided — nothing to search on.";
+    readonly recovery: "Provide a free-text query, protein sequence, organism name, experimental method, or maximum resolution.";
 }, {
     readonly reason: "duplicate_dimension";
     readonly code: JsonRpcErrorCode.InvalidParams;
@@ -66,6 +68,8 @@ export declare const searchStructures: import("@cyanheads/mcp-ts-core").ToolDefi
     readonly recovery: "List each facet dimension at most once; drop the repeated value and re-call.";
 }], {
     readonly totalCount: z.ZodNumber;
+    readonly start: z.ZodNumber;
+    readonly nextStart: z.ZodOptional<z.ZodNumber>;
     readonly effectiveQuery: z.ZodOptional<z.ZodString>;
     readonly notice: z.ZodOptional<z.ZodString>;
 }>;

package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"search-structures.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-structures.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAqCjE,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAsP3B,CAAC"}

package/dist/mcp-server/tools/definitions/search-structures.tool.js CHANGED Viewed

@@ -46,8 +46,8 @@ export const searchStructures = tool('protein_search_structures', {
         {
             reason: 'no_criteria',
             code: JsonRpcErrorCode.InvalidParams,
-            when: 'No query, sequence, or organism was provided — nothing to search on.',
-            recovery: 'Provide a free-text query, a protein sequence, or an organism name (filters alone are not enough).',
+            when: 'No query, sequence, organism, method, or maximum resolution was provided — nothing to search on.',
+            recovery: 'Provide a free-text query, protein sequence, organism name, experimental method, or maximum resolution.',
         },
         {
             reason: 'duplicate_dimension',
@@ -98,12 +98,22 @@ export const searchStructures = tool('protein_search_structures', {
             .optional()
             .describe('Optional dimensions to summarize as a facet breakdown alongside the hits. Each dimension at most once; repeating one is rejected.'),
         limit: z.number().int().min(1).max(100).default(25).describe('Maximum hits to return (1–100).'),
+        start: z
+            .number()
+            .int()
+            .min(0)
+            .default(0)
+            .describe('Zero-based result offset. Combine with limit to retrieve later pages.'),
     }),
     output: z.object({
         hits: z
             .array(z
             .object({
             id: z.string().describe('Structure identifier (PDB entry ID or computed-model ID).'),
+            entityId: z
+                .string()
+                .optional()
+                .describe('Matched polymer-entity ID for experimental sequence hits; id remains the chainable PDB entry ID.'),
             source: z
                 .enum(['experimental', 'predicted'])
                 .describe('Which universe the hit came from.'),
@@ -135,6 +145,11 @@ export const searchStructures = tool('protein_search_structures', {
     }),
     enrichment: {
         totalCount: z.number().describe('Total matches upstream before pagination.'),
+        start: z.number().describe('Zero-based offset of the returned page.'),
+        nextStart: z
+            .number()
+            .optional()
+            .describe('Offset for the next page; absent on the final or past-end page.'),
         effectiveQuery: z.string().optional().describe('Echoed text query for follow-up calls.'),
         notice: z
             .string()
@@ -142,8 +157,12 @@ export const searchStructures = tool('protein_search_structures', {
             .describe('Advisory note (empty results, predicted-search caveats, truncation, facet dimensions whose buckets cover materially less than totalCount). Carries every applicable advisory in one string.'),
     },
     async handler(input, ctx) {
-        if (!input.query && !input.sequence && !input.organism) {
-            throw ctx.fail('no_criteria', 'Provide a query, sequence, or organism to search on.', {
+        if (!input.query &&
+            !input.sequence &&
+            !input.organism &&
+            !input.method &&
+            typeof input.max_resolution !== 'number') {
+            throw ctx.fail('no_criteria', 'Provide a query, sequence, organism, method, or maximum resolution to search on.', {
                 ...ctx.recoveryFor('no_criteria'),
             });
         }
@@ -168,6 +187,7 @@ export const searchStructures = tool('protein_search_structures', {
             ...(typeof input.max_evalue === 'number' ? { maxEvalue: input.max_evalue } : {}),
             contentType: CONTENT_TYPE_SCOPES[input.content_type],
             limit: input.limit,
+            start: input.start,
         }, ctx, facetSpecs);
         const experimentalIds = [
             ...new Set(result.hits.filter((h) => !isPredictedId(h.id)).map((h) => entryIdOf(h.id))),
@@ -177,9 +197,14 @@ export const searchStructures = tool('protein_search_structures', {
             for (const meta of await rcsb.getEntries(experimentalIds, ctx))
                 metaById.set(meta.id, meta);
         }
-        const hits = result.hits.map((h) => toHit(h, metaById));
+        const hits = result.hits.map((h) => toHit(h, metaById, Boolean(input.sequence)));
         const facets = result.facets?.map((f) => toFacetOutput(f, cfg.facetBucketCap, result.total));
         ctx.enrich.total(result.total);
+        const nextStart = input.start + hits.length;
+        ctx.enrich({
+            start: input.start,
+            ...(nextStart < result.total ? { nextStart } : {}),
+        });
         if (input.query)
             ctx.enrich.echo(input.query);
         // `notice` is a single last-wins field, so the zero-hit advice and one
@@ -200,6 +225,7 @@ export const searchStructures = tool('protein_search_structures', {
             if (h.title)
                 lines.push(h.title);
             const meta = [
+                h.entityId ? `**Entity:** ${h.entityId}` : null,
                 h.method ? `**Method:** ${h.method}` : null,
                 typeof h.resolution === 'number' ? `**Resolution:** ${h.resolution} Å` : null,
                 h.organism ? `**Organism:** ${h.organism}` : null,
@@ -217,7 +243,7 @@ export const searchStructures = tool('protein_search_structures', {
     },
 });
 /** Build one output hit, folding in enrichment metadata when available. */
-function toHit(hit, metaById) {
+function toHit(hit, metaById, sequenceSearch) {
     if (isPredictedId(hit.id)) {
         const accession = accessionFromCsm(hit.id);
         return {
@@ -227,9 +253,11 @@ function toHit(hit, metaById) {
             ...(accession ? { uniprotAccession: accession } : {}),
         };
     }
-    const meta = metaById.get(entryIdOf(hit.id));
+    const entryId = entryIdOf(hit.id);
+    const meta = metaById.get(entryId);
     return {
-        id: hit.id,
+        id: sequenceSearch ? entryId : hit.id,
+        ...(sequenceSearch ? { entityId: hit.id } : {}),
         source: 'experimental',
         score: hit.score,
         ...(meta?.title ? { title: meta.title } : {}),

package/dist/mcp-server/tools/definitions/search-structures.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/track-ligands.tool.d.ts CHANGED Viewed

@@ -17,6 +17,7 @@ export declare const trackLigands: import("@cyanheads/mcp-ts-core").ToolDefiniti
     comp_id: z.ZodOptional<z.ZodString>;
     pdb_id: z.ZodOptional<z.ZodString>;
     limit: z.ZodDefault<z.ZodNumber>;
+    start: z.ZodDefault<z.ZodNumber>;
 }, z.core.$strip>, z.ZodObject<{
     mode: z.ZodEnum<{
         binding_site: "binding_site";
@@ -59,6 +60,8 @@ export declare const trackLigands: import("@cyanheads/mcp-ts-core").ToolDefiniti
     readonly recovery: "Use mode \"find_ligand\" to resolve a name to a component ID first, then confirm the ligand is present in the structure via protein_get_structure.";
 }], {
     readonly totalCount: z.ZodOptional<z.ZodNumber>;
+    readonly start: z.ZodOptional<z.ZodNumber>;
+    readonly nextStart: z.ZodOptional<z.ZodNumber>;
     readonly resolvedCompId: z.ZodOptional<z.ZodString>;
     readonly notice: z.ZodOptional<z.ZodString>;
 }>;

package/dist/mcp-server/tools/definitions/track-ligands.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"track-ligands.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/track-ligands.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA0CjE,eAAO,MAAM,YAAY~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAuOvB~~,CAAC"}
1	+ {"version":3,"file":"track-ligands.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/track-ligands.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA0CjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAgQvB,CAAC"}

package/dist/mcp-server/tools/definitions/track-ligands.tool.js CHANGED Viewed

@@ -82,6 +82,12 @@ export const trackLigands = tool('protein_track_ligands', {
             .max(100)
             .default(25)
             .describe('Maximum results to return (1–100).'),
+        start: z
+            .number()
+            .int()
+            .min(0)
+            .default(0)
+            .describe('Zero-based result offset (mode structures_with_ligand only).'),
     }),
     output: z.object({
         mode: z
@@ -113,6 +119,14 @@ export const trackLigands = tool('protein_track_ligands', {
             .number()
             .optional()
             .describe('Total upstream matches before pagination (structures_with_ligand).'),
+        start: z
+            .number()
+            .optional()
+            .describe('Zero-based offset of the structures_with_ligand result page.'),
+        nextStart: z
+            .number()
+            .optional()
+            .describe('Offset for the next structures_with_ligand page; absent on the final or past-end page.'),
         resolvedCompId: z.string().optional().describe('The chemical component ID used to query.'),
         notice: z
             .string()
@@ -161,9 +175,14 @@ export const trackLigands = tool('protein_track_ligands', {
                 throw ctx.fail('missing_param', 'mode structures_with_ligand requires a "comp_id".', {
                     ...ctx.recoveryFor('missing_param'),
                 });
-            const result = await rcsb.searchByLigand(compId, { limit: input.limit }, ctx);
+            const result = await rcsb.searchByLigand(compId, { limit: input.limit, start: input.start }, ctx);
             ctx.enrich.total(result.total);
-            ctx.enrich({ resolvedCompId: compId });
+            const nextStart = input.start + result.hits.length;
+            ctx.enrich({
+                resolvedCompId: compId,
+                start: input.start,
+                ...(nextStart < result.total ? { nextStart } : {}),
+            });
             // A valid component with zero containing structures is an empty result set,
             // not a not-found — mirrors protein_search_structures' empty-hits behavior.
             if (result.hits.length === 0) {

package/dist/mcp-server/tools/definitions/track-ligands.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/services/rcsb/rcsb-service.d.ts CHANGED Viewed

@@ -40,6 +40,7 @@ export declare class RcsbService {
         maxEvalue?: number;
         minIdentity?: number;
         limit?: number;
+        start?: number;
         contentType?: ContentType[];
     }, ctx: Context): Promise<SearchResult>;
     /**
@@ -51,6 +52,7 @@ export declare class RcsbService {
      */
     searchByLigand(compId: string, opts: {
         limit?: number;
+        start?: number;
         contentType?: ContentType[];
     }, ctx: Context): Promise<SearchResult>;
     /**

package/dist/services/rcsb/rcsb-service.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/rcsb/rcsb-service.js CHANGED Viewed

@@ -64,7 +64,7 @@ export class RcsbService {
             return_type: 'polymer_entity',
             request_options: {
                 ...contentTypeOption(opts.contentType),
-                paginate: { start: 0, rows: opts.limit ?? 25 },
+                paginate: { start: opts.start ?? 0, rows: opts.limit ?? 25 },
                 scoring_strategy: 'sequence',
             },
         };
@@ -79,7 +79,7 @@ export class RcsbService {
      * entries, not an arbitrary PDB-ID-ascending slice).
      */
     async searchByLigand(compId, opts, ctx) {
-        const raw = await this.postSearch(ligandContainmentQuery(compId, opts.contentType, opts.limit ?? 25, true), ctx, 'RcsbService.searchByLigand');
+        const raw = await this.postSearch(ligandContainmentQuery(compId, opts.contentType, opts.start ?? 0, opts.limit ?? 25, true), ctx, 'RcsbService.searchByLigand');
         return { total: raw.total_count ?? 0, hits: normalizeHits(raw.result_set) };
     }
     /**
@@ -88,7 +88,7 @@ export class RcsbService {
      * surfaces first — a count-only query (rows 0), no rows or sort pulled.
      */
     async countEntriesWithLigand(compId, ctx) {
-        const raw = await this.postSearch(ligandContainmentQuery(compId, undefined, 0, false), ctx, 'RcsbService.countEntriesWithLigand');
+        const raw = await this.postSearch(ligandContainmentQuery(compId, undefined, 0, 0, false), ctx, 'RcsbService.countEntriesWithLigand');
         return raw.total_count ?? 0;
     }
     /** Resolve a ligand name/synonym to candidate chemical component IDs. */
@@ -309,7 +309,7 @@ function contentTypeOption(contentTypes) {
  * `rows` bounds the page (0 for a count-only query), and `sortByResolution`
  * orders entries best-resolution-first (skip it for counts — order is moot).
  */
-function ligandContainmentQuery(compId, contentType, rows, sortByResolution) {
+function ligandContainmentQuery(compId, contentType, start, rows, sortByResolution) {
     return {
         query: {
             type: 'terminal',
@@ -323,7 +323,7 @@ function ligandContainmentQuery(compId, contentType, rows, sortByResolution) {
         return_type: 'entry',
         request_options: {
             ...contentTypeOption(contentType ?? ['experimental']),
-            paginate: { start: 0, rows },
+            paginate: { start, rows },
             ...(sortByResolution
                 ? { sort: [{ sort_by: 'rcsb_entry_info.resolution_combined', direction: 'asc' }] }
                 : {}),

package/dist/services/rcsb/rcsb-service.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/protein-mcp-server",
-  "version": "0.5.2",
+  "version": "0.5.3",
   "mcpName": "io.github.cyanheads/protein-mcp-server",
   "description": "Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.",
   "type": "module",

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/protein-mcp-server",
     "source": "github"
   },
-  "version": "0.5.2",
+  "version": "0.5.3",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.5.2",
+      "version": "0.5.3",
       "packageArguments": [
         {
           "type": "positional",
@@ -48,7 +48,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.5.2",
+      "version": "0.5.3",
       "packageArguments": [
         {
           "type": "positional",