protein-mcp-server
Reach for this one when a question touches protein structures and you'd rather not stitch together RCSB, AlphaFold DB, UniProt, InterPro, and Foldseek by hand. Seven tools cover the workflow: search experimental and predicted structures by text, sequence, organism, method, or resolution; fetch metadata and coordinate URLs; find sequence or fold homologs; track ligands and their binding sites; align structures with TM-align or jFATCAT; profile PDB holdings as counts and timelines; and pull UniProt features with InterPro domains and GO terms. It runs over stdio or Streamable HTTP, needs no API key, and a hosted instance is available if you'd rather not run it locally. The main thing to read in the docs is the identifier rules, since PDB entries, UniProt accessions, and AlphaFold IDs each route to different sources.
- tools
- 7
- transport
- HTTP
- last updated
- Jul 10, 2026
Tools
7 toolsPublic tool metadata for what this MCP can expose to an agent.
protein_search_structuresSearch experimental and predicted structures by text, sequence, or organism/method/resolution, with optional facets
Search experimental and predicted structures by text, sequence, or organism/method/resolution, with optional facets
No parameter schema in public metadata yet.
protein_get_structureFetch metadata and coordinate URLs for experimental, predicted, or best-available structures
Fetch metadata and coordinate URLs for experimental, predicted, or best-available structures
No parameter schema in public metadata yet.
protein_find_similarFind sequence homologs (RCSB mmseqs2) or fold homologs (Foldseek)
Find sequence homologs (RCSB mmseqs2) or fold homologs (Foldseek)
No parameter schema in public metadata yet.
protein_track_ligandsResolve ligands to component IDs, find structures containing one, or map its binding site
Resolve ligands to component IDs, find structures containing one, or map its binding site
No parameter schema in public metadata yet.
protein_compare_structuresAlign structures with TM-align or jFATCAT, against a reference or all pairs
Align structures with TM-align or jFATCAT, against a reference or all pairs
No parameter schema in public metadata yet.
protein_analyze_collectionProfile the PDB as counts, histograms, timelines, and cross-tabs
Profile the PDB as counts, histograms, timelines, and cross-tabs
No parameter schema in public metadata yet.
protein_get_annotationsFetch UniProt features and variants plus InterPro domains with GO terms
Fetch UniProt features and variants plus InterPro domains with GO terms
No parameter schema in public metadata yet.
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@cyanheads/protein-mcp-server
Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.
Details
- Repository
- github.com/cyanheads/protein-mcp-server
- Website
- protein.caseyjhand.com/mcp
- Transport
- HTTP
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