npm - @cyanheads/protein-mcp-server - Versions diffs - 0.8.2 → 0.8.4 - Mend

@cyanheads/protein-mcp-server 0.8.2 → 0.8.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (51) hide show

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

@@ -20,11 +20,13 @@ export class RcsbService {
     graphqlUrl;
     dataRestBase;
     filesBase;
+    modelsBase;
     constructor(_config, _storage, serverConfig) {
         this.searchUrl = `${serverConfig.rcsbSearchBaseUrl}/rcsbsearch/v2/query`;
         this.graphqlUrl = `${serverConfig.rcsbDataBaseUrl}/graphql`;
         this.dataRestBase = `${serverConfig.rcsbDataBaseUrl}/rest/v1/core`;
         this.filesBase = serverConfig.rcsbFilesBaseUrl;
+        this.modelsBase = serverConfig.rcsbModelsBaseUrl;
     }
     // ─── Search ────────────────────────────────────────────────────────────────
     /** Full-text / filtered structure search, optionally with a facet breakdown. */
@@ -225,9 +227,30 @@ export class RcsbService {
         return normalizeChemComp(id, raw);
     }
     // ─── Files ────────────────────────────────────────────────────────────────────
-    /** Construct a coordinate-file download URL for a PDB entry. */
-    coordinateFileUrl(pdbId, format) {
-        return `${this.filesBase}/download/${pdbId.toUpperCase()}.${format}`;
+    /**
+     * Coordinate-file URLs RCSB serves for an entry. mmCIF and PDB format come from
+     * the file-download host, BinaryCIF only from the ModelServer host. The PDB
+     * format is omitted when the entry reports it is not PDB-format compatible
+     * (large entries archived as mmCIF only); an unreported value keeps it. A
+     * computed model is not in the file-download archive at all, so only its
+     * BinaryCIF is listed — its provider publishes the text formats.
+     */
+    coordinateUrls(entry) {
+        const id = entry.id.toUpperCase();
+        const bcif = `${this.modelsBase}/${id}.bcif`;
+        if (entry.computedModelProvider)
+            return { bcif };
+        return {
+            cif: this.mmcifUrl(id),
+            ...(entry.pdbFormatCompatible === false
+                ? {}
+                : { pdb: `${this.filesBase}/download/${id}.pdb` }),
+            bcif,
+        };
+    }
+    /** mmCIF download URL for an experimental entry — the one text format every entry has. */
+    mmcifUrl(pdbId) {
+        return `${this.filesBase}/download/${pdbId.toUpperCase()}.cif`;
     }
     // ─── Private ───────────────────────────────────────────────────────────────────
     postSearch(body, ctx, operation) {
@@ -504,8 +527,10 @@ const CSM_PROVIDER_NAMES = {
     ModelArchive: 'ModelArchive',
 };
 function normalizeEntry(raw) {
-    const sourceDb = raw.rcsb_comp_model_provenance?.source_db;
+    const provenance = raw.rcsb_comp_model_provenance;
+    const sourceDb = provenance?.source_db;
     const computedModelProvider = sourceDb ? (CSM_PROVIDER_NAMES[sourceDb] ?? sourceDb) : undefined;
+    const pdbCompatible = raw.pdbx_database_status?.pdb_format_compatible;
     const polymerEntities = (raw.polymer_entities ?? []).map(normalizePolymerEntity);
     const organisms = [
         ...new Set(polymerEntities.map((e) => e.organism).filter((o) => !!o)),
@@ -518,6 +543,10 @@ function normalizeEntry(raw) {
     return {
         id: raw.rcsb_id,
         ...(computedModelProvider ? { computedModelProvider } : {}),
+        ...(provenance?.entry_id ? { computedModelEntryId: provenance.entry_id } : {}),
+        ...(pdbCompatible === 'Y' || pdbCompatible === 'N'
+            ? { pdbFormatCompatible: pdbCompatible === 'Y' }
+            : {}),
         ...(raw.struct?.title ? { title: raw.struct.title } : {}),
         ...(methods.length > 0 ? { methods } : {}),
         ...(typeof resolution === 'number' ? { resolution } : {}),
@@ -601,7 +630,8 @@ const ENTRIES_QUERY = `query Entries($ids: [String!]!) {
     rcsb_id
     struct { title }
     exptl { method }
-    rcsb_comp_model_provenance { source_db }
+    pdbx_database_status { pdb_format_compatible }
+    rcsb_comp_model_provenance { source_db entry_id }
     rcsb_entry_info { resolution_combined molecular_weight }
     rcsb_accession_info { initial_release_date }
     polymer_entities {

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

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

@@ -103,6 +103,12 @@ export interface LigandMeta {
 }
 /** Normalized entry-level metadata from the GraphQL batch. */
 export interface EntryMeta {
+    /**
+     * The modelling provider's own ID for a computed model (e.g. `AF-P69905-F1`,
+     * `ma-asfv-asfvg-001`) — the key its coordinate files are published under.
+     * Absent for experimental entries.
+     */
+    computedModelEntryId?: string;
     /**
      * Modelling provider display name when this ID is a computed structure model
      * (`AF_*` / `MA_*`) rather than an experimental entry — e.g. "AlphaFold DB",
@@ -120,6 +126,12 @@ export interface EntryMeta {
     molecularWeight?: number;
     /** Distinct source organisms across polymer entities. */
     organisms: string[];
+    /**
+     * Whether the archive publishes a legacy PDB-format file for this entry —
+     * `false` for large entries archived as mmCIF only. Absent when the record
+     * reports no value (computed models).
+     */
+    pdbFormatCompatible?: boolean;
     /** Modeled polymer entities. */
     polymerEntities: PolymerEntityMeta[];
     /** Initial release date (ISO 8601). */
@@ -129,6 +141,15 @@ export interface EntryMeta {
     /** Structure title. */
     title?: string;
 }
+/** Coordinate-file download URLs by format; a format with no working file is absent. */
+export interface CoordinateUrls {
+    /** Binary CIF. */
+    bcif?: string;
+    /** mmCIF. */
+    cif?: string;
+    /** Legacy PDB format. */
+    pdb?: string;
+}
 /** One protein residue lining a ligand's binding pocket. */
 export interface BindingResidue {
     /** Author/asym chain ID the residue belongs to. */

package/dist/services/rcsb/types.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../../src/services/rcsb/types.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,sDAAsD;AACtD,MAAM,WAAW,SAAS;IACxB,qFAAqF;IACrF,EAAE,EAAE,MAAM,CAAC;IACX,4BAA4B;IAC5B,KAAK,EAAE,MAAM,CAAC;CACf;AAED,mFAAmF;AACnF,MAAM,WAAW,WAAW;IAC1B;;;;;;;OAOG;IACH,KAAK,CAAC,EAAE,cAAc,CAAC;IACvB,sCAAsC;IACtC,KAAK,EAAE,MAAM,CAAC;IACd,mEAAmE;IACnE,KAAK,EAAE,MAAM,CAAC;IACd;;;;OAIG;IACH,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB;;;;OAIG;IACH,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAED,yCAAyC;AACzC,MAAM,WAAW,cAAc;IAC7B,uDAAuD;IACvD,SAAS,EAAE,MAAM,CAAC;IAClB,yFAAyF;IACzF,OAAO,EAAE,WAAW,EAAE,CAAC;IACvB,2EAA2E;IAC3E,SAAS,EAAE,MAAM,CAAC;IAClB,gEAAgE;IAChE,SAAS,CAAC,EAAE,OAAO,CAAC;CACrB;AAED,oCAAoC;AACpC,MAAM,WAAW,YAAY;IAC3B,+CAA+C;IAC/C,MAAM,CAAC,EAAE,cAAc,EAAE,CAAC;IAC1B,gCAAgC;IAChC,IAAI,EAAE,SAAS,EAAE,CAAC;IAClB,kDAAkD;IAClD,KAAK,EAAE,MAAM,CAAC;CACf;AAED,kEAAkE;AAClE,MAAM,WAAW,iBAAiB;IAChC;;;OAGG;IACH,WAAW,CAAC,EAAE,MAAM,EAAE,CAAC;IACvB,+DAA+D;IAC/D,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,yCAAyC;IACzC,QAAQ,EAAE,MAAM,CAAC;IACjB;;;;OAIG;IACH,YAAY,CAAC,EAAE,MAAM,EAAE,CAAC;IACxB,uCAAuC;IACvC,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,8EAA8E;IAC9E,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,4CAA4C;IAC5C,cAAc,CAAC,EAAE,MAAM,CAAC;CACzB;AAED,mGAAmG;AACnG,MAAM,WAAW,WAAW;IAC1B,6CAA6C;IAC7C,SAAS,EAAE,MAAM,CAAC;IAClB,4EAA4E;IAC5E,MAAM,EAAE,MAAM,EAAE,CAAC;IACjB,oEAAoE;IACpE,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB;AAED,8DAA8D;AAC9D,MAAM,WAAW,UAAU;IACzB,iDAAiD;IACjD,MAAM,EAAE,MAAM,CAAC;IACf,wCAAwC;IACxC,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,oCAAoC;IACpC,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAED,8DAA8D;AAC9D,MAAM,WAAW,SAAS;IACxB;;;;OAIG;IACH,oBAAoB,CAAC,EAAE,MAAM,CAAC;IAC9B;;;;;OAKG;IACH,qBAAqB,CAAC,EAAE,MAAM,CAAC;IAC/B,oBAAoB;IACpB,EAAE,EAAE,MAAM,CAAC;IACX,4CAA4C;IAC5C,OAAO,EAAE,UAAU,EAAE,CAAC;IACtB,2DAA2D;IAC3D,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACnB,kDAAkD;IAClD,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,yDAAyD;IACzD,SAAS,EAAE,MAAM,EAAE,CAAC;IACpB;;;;OAIG;IACH,mBAAmB,CAAC,EAAE,OAAO,CAAC;IAC9B,gCAAgC;IAChC,eAAe,EAAE,iBAAiB,EAAE,CAAC;IACrC,uCAAuC;IACvC,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,4CAA4C;IAC5C,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,uBAAuB;IACvB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,wFAAwF;AACxF,MAAM,WAAW,cAAc;IAC7B,kBAAkB;IAClB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,aAAa;IACb,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,yBAAyB;IACzB,GAAG,CAAC,EAAE,MAAM,CAAC;CACd;AAED,4DAA4D;AAC5D,MAAM,WAAW,cAAc;IAC7B,mDAAmD;IACnD,MAAM,EAAE,MAAM,CAAC;IACf,2CAA2C;IAC3C,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,kDAAkD;IAClD,aAAa,EAAE,MAAM,CAAC;IACtB,wCAAwC;IACxC,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,4DAA4D;AAC5D,MAAM,WAAW,WAAW;IAC1B,uCAAuC;IACvC,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,oCAAoC;IACpC,YAAY,EAAE,MAAM,CAAC;IACrB,mDAAmD;IACnD,QAAQ,EAAE,cAAc,EAAE,CAAC;CAC5B;AAED,gDAAgD;AAChD,MAAM,WAAW,QAAQ;IACvB,iCAAiC;IACjC,MAAM,EAAE,MAAM,CAAC;IACf,yBAAyB;IACzB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,2BAA2B;IAC3B,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,+BAA+B;IAC/B,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,qBAAqB;IACrB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,sCAAsC;IACtC,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,2CAA2C;IAC3C,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAED,wDAAwD;AACxD,MAAM,MAAM,WAAW,GAAG,cAAc,GAAG,eAAe,CAAC;AAE3D,uEAAuE;AACvE,MAAM,WAAW,qBAAqB;IACpC;;;;OAIG;IACH,WAAW,CAAC,EAAE,WAAW,EAAE,CAAC;IAC5B,iBAAiB;IACjB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,wCAAwC;IACxC,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,+BAA+B;IAC/B,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,6DAA6D;IAC7D,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,4DAA4D;IAC5D,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,gDAAgD;IAChD,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,2DAA2D;IAC3D,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,mBAAmB;IACnB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,uBAAuB;IACvB,IAAI,CAAC,EAAE,MAAM,CAAC;CACf"}

package/dist/services/shared/identifiers.d.ts CHANGED Viewed

@@ -14,6 +14,13 @@ export declare function isUniProtAccession(value: string): boolean;
 export declare function isAlphaFoldEntryId(value: string): boolean;
 /** True when `value` is a syntactically valid PDB entry ID. */
 export declare function isPdbId(value: string): boolean;
-/** Extract the PDB entry ID from a polymer-entity ID (`4HHB_1` → `4HHB`). */
+/** True when `value` is an RCSB computed-model ID (`AF_*` AlphaFold / `MA_*` ModelArchive). */
+export declare function isComputedModelId(value: string): boolean;
+/**
+ * Extract the entry ID from a polymer-entity ID (`4HHB_1` → `4HHB`). A
+ * computed-model ID carries its own underscore after the `AF_`/`MA_` prefix, so
+ * only its trailing `_<entity number>` is stripped (`AF_AFP69905F1_1` →
+ * `AF_AFP69905F1`); a bare computed-model entry ID passes through.
+ */
 export declare function entryIdOf(identifier: string): string;
 //# sourceMappingURL=identifiers.d.ts.map

package/dist/services/shared/identifiers.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"identifiers.d.ts","sourceRoot":"","sources":["../../../src/services/shared/identifiers.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAcH,oEAAoE;AACpE,wBAAgB,kBAAkB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAEzD;AAED;;;;;GAKG;AACH,wBAAgB,kBAAkB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAEzD;AAED,+DAA+D;AAC/D,wBAAgB,OAAO,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAE9C;AAED,~~6EAA6E~~;~~AAC7E~~,wBAAgB,SAAS,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,~~CAGpD~~"}
1	+ {"version":3,"file":"identifiers.d.ts","sourceRoot":"","sources":["../../../src/services/shared/identifiers.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAcH,oEAAoE;AACpE,wBAAgB,kBAAkB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAEzD;AAED;;;;;GAKG;AACH,wBAAgB,kBAAkB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAEzD;AAED,+DAA+D;AAC/D,wBAAgB,OAAO,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAE9C;AAED,+FAA+F;AAC/F,wBAAgB,iBAAiB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAExD;AAED;;;;;GAKG;AACH,wBAAgB,SAAS,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAIpD"}

package/dist/services/shared/identifiers.js CHANGED Viewed

@@ -28,8 +28,19 @@ export function isAlphaFoldEntryId(value) {
 export function isPdbId(value) {
     return PDB_RE.test(value.trim());
 }
-/** Extract the PDB entry ID from a polymer-entity ID (`4HHB_1` → `4HHB`). */
+/** True when `value` is an RCSB computed-model ID (`AF_*` AlphaFold / `MA_*` ModelArchive). */
+export function isComputedModelId(value) {
+    return /^(AF|MA)_/i.test(value);
+}
+/**
+ * Extract the entry ID from a polymer-entity ID (`4HHB_1` → `4HHB`). A
+ * computed-model ID carries its own underscore after the `AF_`/`MA_` prefix, so
+ * only its trailing `_<entity number>` is stripped (`AF_AFP69905F1_1` →
+ * `AF_AFP69905F1`); a bare computed-model entry ID passes through.
+ */
 export function entryIdOf(identifier) {
+    if (isComputedModelId(identifier))
+        return identifier.replace(/_\d+$/, '').toUpperCase();
     const base = identifier.split(/[_.]/)[0] ?? identifier;
     return base.toUpperCase();
 }

package/dist/services/shared/identifiers.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"identifiers.js","sourceRoot":"","sources":["../../../src/services/shared/identifiers.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,qEAAqE;AACrE,MAAM,YAAY,GAAG,4EAA4E,CAAC;AAElG,4DAA4D;AAC5D,MAAM,UAAU,GAAG,IAAI,MAAM,CAAC,IAAI,YAAY,GAAG,EAAE,GAAG,CAAC,CAAC;AAExD,uFAAuF;AACvF,MAAM,WAAW,GAAG,IAAI,MAAM,CAAC,OAAO,YAAY,SAAS,EAAE,GAAG,CAAC,CAAC;AAElE,wFAAwF;AACxF,MAAM,MAAM,GAAG,uBAAuB,CAAC;AAEvC,oEAAoE;AACpE,MAAM,UAAU,kBAAkB,CAAC,KAAa;IAC9C,OAAO,UAAU,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;AACvC,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,kBAAkB,CAAC,KAAa;IAC9C,OAAO,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;AACxC,CAAC;AAED,+DAA+D;AAC/D,MAAM,UAAU,OAAO,CAAC,KAAa;IACnC,OAAO,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;AACnC,CAAC;AAED,~~6EAA6E~~;~~AAC7E~~,MAAM,UAAU,SAAS,CAAC,UAAkB;IAC1C,MAAM,IAAI,GAAG,UAAU,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,IAAI,UAAU,CAAC;IACvD,OAAO,IAAI,CAAC,WAAW,EAAE,CAAC;AAC5B,CAAC"}
1	+ {"version":3,"file":"identifiers.js","sourceRoot":"","sources":["../../../src/services/shared/identifiers.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,qEAAqE;AACrE,MAAM,YAAY,GAAG,4EAA4E,CAAC;AAElG,4DAA4D;AAC5D,MAAM,UAAU,GAAG,IAAI,MAAM,CAAC,IAAI,YAAY,GAAG,EAAE,GAAG,CAAC,CAAC;AAExD,uFAAuF;AACvF,MAAM,WAAW,GAAG,IAAI,MAAM,CAAC,OAAO,YAAY,SAAS,EAAE,GAAG,CAAC,CAAC;AAElE,wFAAwF;AACxF,MAAM,MAAM,GAAG,uBAAuB,CAAC;AAEvC,oEAAoE;AACpE,MAAM,UAAU,kBAAkB,CAAC,KAAa;IAC9C,OAAO,UAAU,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;AACvC,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,kBAAkB,CAAC,KAAa;IAC9C,OAAO,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;AACxC,CAAC;AAED,+DAA+D;AAC/D,MAAM,UAAU,OAAO,CAAC,KAAa;IACnC,OAAO,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;AACnC,CAAC;AAED,+FAA+F;AAC/F,MAAM,UAAU,iBAAiB,CAAC,KAAa;IAC7C,OAAO,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;AAClC,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,SAAS,CAAC,UAAkB;IAC1C,IAAI,iBAAiB,CAAC,UAAU,CAAC;QAAE,OAAO,UAAU,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,WAAW,EAAE,CAAC;IACxF,MAAM,IAAI,GAAG,UAAU,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,IAAI,UAAU,CAAC;IACvD,OAAO,IAAI,CAAC,WAAW,EAAE,CAAC;AAC5B,CAAC"}

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/protein-mcp-server",
-  "version": "0.8.2",
+  "version": "0.8.4",
   "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": "0.8.2",
+  "version": "0.8.4",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.8.2",
+      "version": "0.8.4",
       "packageArguments": [
         {
           "type": "positional",
@@ -48,7 +48,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.8.2",
+      "version": "0.8.4",
       "packageArguments": [
         {
           "type": "positional",