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PDBe MCP Servers

PDBe MCP Servers

Official
by PDBeurope

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    Related Servers

    • A
      license
      Not graded
      quality
      B
      maintenance
      Enables AI agents to query Protein Data Bank in Europe (EBI) structural data by 4-character PDB ID, retrieving entry summaries, molecule/entity listings with chain lengths, and SIFTS cross-database mappings to UniProt accessions and residue ranges. Runs as a hosted gateway endpoint or a local stdio server with no authentication required.
      215 npm
      MIT
    • A
      license
      B
      quality
      D
      maintenance
      Enables searching, retrieving, and downloading protein structure data from the RCSB Protein Data Bank. Supports intelligent protein structure search, comprehensive data retrieval, and multiple file format downloads for bioinformatics research.
      3
      MIT
    • F
      license
      Not graded
      quality
      Not graded
      maintenance
      Enables interaction with the RCSB Protein Data Bank to search, analyze, and visualize protein structures. It provides specialized tools for downloading coordinate files and performing structural modifications like residue mutations and metal atom replacements.
      -
    • F
      license
      B
      quality
      D
      maintenance
      Provides programmatic access to AlphaFold protein structure predictions and UniProt data, enabling users to retrieve protein structures, summaries, and annotations through natural language.
      3
      -
    • A
      license
      Not graded
      quality
      C
      maintenance
      Provides access to AlphaFold predicted protein 3D structures from EBI, enabling retrieval of prediction metadata, summaries, annotations, and UniProt data.
      323 npm
      1
      MIT

    TDQS

    B3.1/5.0

    Scored across 60 tools

    Disambiguation3/5

    Many tools cover distinct PDBe resource levels (entry, entity, chain, ligand, UniProt, complex, validation, graph), and descriptions generally clarify their targets. However, several retrieval tools overlap conceptually—e.g. multiple ligand interaction tools, bound-molecule tools, and several sequence/annotation endpoints—while cryptic generated names make misselection likely in a 60-tool set.

    Naming Consistency2/5

    There is a shared `ebi-pdbe-` prefix, but the remainder is inconsistent: some tools use clean descriptive names like `search_schema`, `open_structure`, and `graph_nodes`, while many are auto-generated strings with embedded identifiers and hashes such as `seq_cuuscu_acc_a66a4f59` and `comp_intx_comp_intx_hetcode_8fee3085`. Hyphenated and underscored names are also mixed.

    Tool Count2/5

    The server exposes 60 tools, which is very heavy for an agent-facing toolset even though PDBe is a broad structural bioinformatics domain. Many endpoints appear to correspond to individual PDBe API resources, increasing selection burden and reducing practical usability compared with a more curated set.

    Completeness4/5

    Coverage is broad: search, entry-level summaries, entities/chains, sequences, ligands, interactions, validation, UniProt mappings, complexes, Rfam, graph schema helpers, and visualization/workspace tools are all represented. Some direct access patterns are missing or only reachable indirectly through search, but there are few obvious dead ends.

    Maintenance

    ActivityMaintained
    ResponsivenessLimited data