protein-mcp-server MCP Server

MCP Server for 3D protein structural data retrieval & analysis from RCSB PDB, PDBe, and UniProt.

Publisher claimed. No tool list reported, and Pod has not connected to this server.

Status

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Connect

Published as protein-mcp-server on npm. Runs locally.

Known issues

54 problems reported by people outside the maintainer team. Issues filed by the project's own owners, members and collaborators are excluded — those are release checklists and internal refactors, not things that will go wrong for you. Showing 12.

Most discussed

feat(search): add retrieval for bounded RCSB result sets

Use case

protein_search_structures, protein_find_similar with by: "sequence", and protein_track_ligands with mode: "structures_with_ligand" expose totalCount but accept only limit. A caller cannot request a later RCSB page without leaving the server.

Proposed behavior

Add an optional start input to those three RCSB-backed result modes. start is a zero-based result offset, defaults to 0, and combines with the existing limit (1–100). The name matches RCSB Search AP

Read the thread · 2026-08-17 · closed · 2 comments

feat(protein_analyze_collection): disclose combined cross-tab bucket size

Use case

protein_analyze_collection applies the same bucket_limit cap independently to the parent dimension and to the nested cross-tab child, so a two-dimension group_by can return up to cap² buckets. At the default cap of 50 that is up to 2,500 buckets in one response; at the maximum it is larger still.

Each position honestly discloses its own truncation — the parent dimension carries truncated, and so does each child — so nothing is hidden from a caller who inspects every leve

Read the thread · 2026-08-17 · closed · 2 comments

bug(protein_analyze_collection): group_by accepts the same dimension twice

Server version

0.4.2

mcp-ts-core version

^0.11.5

Runtime

Bun

Runtime version

Bun 1.3.14

Transport

HTTP (Streamable HTTP)

OS

macOS 26.1

Description

protein_analyze_collection accepts the same dimension twice in group_by. {"group_by": ["method", "method"]} passes schema validation and reaches buildFacetSpec('method', interval, 'method'), which builds a method facet nested inside itself and sends that to RCSB.

Verified live against RCSB, the self-ne

Read the thread · 2026-08-16 · closed · 2 comments

feat(facets): nested cross-tab child is single-valued, not an array

Use case

The facet output schema advertises buckets[].children as an unbounded array of nested dimensions, but no code path can produce more than one element. Three independent bounds enforce that:

FacetSpec.child (src/services/rcsb/rcsb-service.ts) is a single optional spec, not a list.
toRcsbFacet requests exactly one nested facet: if (spec.child) facet.facets = [toRcsbFacet(spec.child)].
normalizeBuckets reads only index 0 of the upstream response and wraps the result

Read the thread · 2026-08-16 · closed · 2 comments

enhancement(protein_track_ligands): structures_with_ligand score is a constant; sort is undocumented

protein_track_ligands mode structures_with_ligand returns a score on every entry that carries no signal, and an ordering that isn't stated.

Observed

{ mode: "structures_with_ligand", comp_id: "HEM", limit: 8 } → every row scores 1.00, ordered by PDB ID ascending (101M, 102M, 103M … — myoglobins ahead of any hemoglobin). Containment is boolean (an entry either has the component or doesn't), so RCSB's relevance score is uniform and the column is noise; the PDB-ascending order is

Read the thread · 2026-07-03 · closed · 2 comments

Most recent

bug(protein_search_structures): sequence-only controls are silently ignored

Server version

0.5.3

mcp-ts-core version

^0.12.3

Runtime

Bun

Runtime version

Bun 1.4.0 / Node v26.5.0

Transport

HTTP (Streamable HTTP)

OS

macOS 26.1

Description

protein_search_structures accepts min_identity and max_evalue without sequence, then silently runs the non-sequence query. A malformed workflow therefore looks filtered even though neither threshold affects the result.

Steps to reproduce

Call protein_search_structures with `{ "q

Read the thread · 2026-08-31 · open · 0 comments

bug(protein_analyze_collection): zero-match scopes omit the declared notice

Server version

0.5.3

mcp-ts-core version

^0.12.3

Runtime

Bun

Runtime version

Bun 1.4.0 / Node v26.5.0

Transport

HTTP (Streamable HTTP)

OS

macOS 26.1

Description

protein_analyze_collection returns an empty success for a zero-match scope without the empty-scope advisory declared by its enrichment contract. The result is technically distinguishable through total: 0, but it gives no recovery guidance.

Steps to reproduce

Call `protein_analyze_coll

Read the thread · 2026-08-31 · open · 0 comments

docs(tools): make catalog descriptions caller-facing

The MCP catalog mixes user-facing contracts with implementation mechanics and audience assumptions. Examples include protein_analyze_collection describing a single upstream call and "no row pull," protein_compare_structures describing its internal fanout/concurrency cap, and an output field saying it lets "an agent" cite a structure.

Related: #38

Proposal

Keep provider identity, limits, partial-success behavior, and resume semantics. Remove API-call counts, internal routing/fanout deta

Read the thread · 2026-08-31 · open · 0 comments

bug(protein_find_similar): completed Foldseek results have no retrieval path

Server version

0.5.3

mcp-ts-core version

^0.12.3

Runtime

Bun

Runtime version

Bun 1.4.0 / Node v26.5.0

Transport

HTTP (Streamable HTTP)

OS

macOS 26.1

Description

protein_find_similar silently slices completed Foldseek results to limit. The response has no total, truncation flag, offset, or reusable completed-job ticket, so hits beyond that cap cannot be retrieved through the server.

Related: #41

Steps to reproduce

Call protein_find_similar

Read the thread · 2026-08-31 · open · 0 comments

bug(protein_search_structures): truncated facets omit recovery guidance

Server version

0.5.3

mcp-ts-core version

^0.12.3

Runtime

Bun

Runtime version

Bun 1.4.0 / Node v26.5.0

Transport

HTTP (Streamable HTTP)

OS

macOS 26.1

Description

protein_search_structures marks a capped facet as truncated: true, but its enrichment omits the promised truncation advisory and gives no route to the remaining buckets.

Related: #13, #41

Steps to reproduce

Call protein_search_structures with `{ "query": "kinase", "facets": ["organ

Read the thread · 2026-08-31 · open · 0 comments

bug(protein_analyze_collection): interval is silently ignored for incompatible dimensions

Server version

0.5.3

mcp-ts-core version

^0.12.3

Runtime

Bun

Runtime version

Bun 1.4.0 / Node v26.5.0

Transport

HTTP (Streamable HTTP)

OS

macOS 26.1

Description

protein_analyze_collection.interval is accepted for every group_by shape, but it only reaches the top-level facet when that facet is a histogram. A terms-only call silently drops it, and a numeric/date child in a cross-tab keeps its default interval.

Related: #15

Steps to reproduce

Read the thread · 2026-08-31 · open · 0 comments

bug(protein_track_ligands): formula queries run as name searches

Server version

0.5.3

mcp-ts-core version

^0.12.3

Runtime

Bun

Runtime version

Bun 1.4.0 / Node v26.5.0

Transport

HTTP (Streamable HTTP)

OS

macOS 26.1

Description

protein_track_ligands advertises find_ligand.query as a chemical name or formula, but formula input is handled as a name search. A caller can receive chemically unrelated component IDs with no indication that the declared formula path was not applied.

Related: #17

Steps to reproduce

Read the thread · 2026-08-31 · open · 0 comments

See all 23 reports Pod holds for protein-mcp-server — of 54 qualified upstream.

Firsthand observations

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