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PDBe MCP Servers

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Alternatives to PDBe MCP Servers

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    Related Servers

    • PDBe MCP Server

      pipeworx-io
      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.
      17 npm
      MIT

    • Protein MCP Server

      gqy20
      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

    • Structural Biology MCP Server

      sanatava
      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.
      -

    • mcp-alphafold

      zeinab-sheikhi
      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
      -

    • mcp-alphafold

      pipeworx-io
      A
      license
      Not graded
      quality
      B
      maintenance
      Provides access to AlphaFold predicted protein 3D structures from EBI, enabling retrieval of prediction metadata, summaries, annotations, and UniProt data.
      27 npm
      1
      MIT
    Deploy Server
    One endpoint for every MCP toolRayrun runs every MCP server behind one URL and holds the credentials. Each call is decided per client, tool, and argument, then recorded.ray.runAd

    TDQS

    B3/5.0

    Scored across 34 tools

    Disambiguation3/5

    Many tools operate at overlapping levels (PDB entry, entity, UniProt accession) for similar concepts like interfaces, annotations, conservation, and variations, making selection ambiguous despite detailed descriptions. For example, interface residues are covered by entity-level, entry-level, and UniProt-level tools; similarly, domain/annotation mappers overlap with dedicated entity tools. Descriptions help but names do not clarify boundaries.

    Naming Consistency2/5

    Names are all snake_case but follow no predictable verb_noun pattern: prefixes mix resource types, actions, and abbreviations (e.g., unip_gen_unipdb, best_soubsu, llm_unip_sum), and each ends with a unique hash. The inconsistent prefixing and embedded identifiers make the set hard to scan and remember.

    Tool Count2/5

    34 tools is excessive for a single MCP server, exceeding the typical 3–15 range. While PDBe is a broad domain, many tools could be consolidated or grouped, and the count feels heavy for an agent to manage effectively.

    Completeness4/5

    The surface covers a wide range of PDBe data: ligands, sequences, mappings, annotations, validation, interfaces, and complexes. Minor gaps exist (e.g., no direct raw structure file retrieval or generic search), but most structural biology queries are supported.

    Maintenance

    ActivityMaintained
    ResponsivenessWithin a week

    Resources