PDBe MCP Servers
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Related Servers
- AlicenseNot gradedqualityBmaintenanceEnables 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 npmMIT
- AlicenseNot gradedqualityCmaintenanceEnables querying and retrieving experimental protein structures from the RCSB Protein Data Bank, including text search, full entry records, polymer entities, ligands, and assemblies.287 npmMIT
- AlicenseBqualityDmaintenanceEnables 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.3MIT
- FlicenseNot gradedqualityNot gradedmaintenanceEnables 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.-
- FlicenseBqualityDmaintenanceProvides programmatic access to AlphaFold protein structure predictions and UniProt data, enabling users to retrieve protein structures, summaries, and annotations through natural language.3-
- AlicenseNot gradedqualityCmaintenanceProvides access to AlphaFold predicted protein 3D structures from EBI, enabling retrieval of prediction metadata, summaries, annotations, and UniProt data.323 npm1MIT
TDQS
Scored across 60 tools
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.
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.
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.
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.