By cyanheads
Federated protein structure & function across experimental (PDB) and predicted (AlphaFold) models.
Scaffold an MCP App tool + UI resource pair. Use when the user asks to add a tool with interactive UI, create an MCP App, or build a visual/interactive tool.
Scaffold a new MCP prompt template. Use when the user asks to add a prompt, create a reusable message template, or define a prompt for LLM interactions.
Scaffold a new MCP resource definition. Use when the user asks to add a resource, expose data via URI, or create a readable endpoint.
Scaffold a new service integration. Use when the user asks to add a service, integrate an external API, or create a reusable domain module with its own initialization and state.
Scaffold a test file for an existing tool, resource, or service. Use when the user asks to add tests, improve coverage, or when a definition exists without a matching test file.
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Federated protein structure & function across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.
Public Hosted Server: https://protein.caseyjhand.com/mcp
Seven tools spanning the structure-research arc — discover, fetch, find homologs, track ligands, compare, profile the corpus, and annotate — over experimental (PDB) and predicted (AlphaFold) structures from one surface:
| Tool | Description |
|---|---|
protein_search_structures | Search experimental and predicted structures by free text, sequence, or organism/method/resolution filters, with optional facet breakdowns. |
protein_get_structure | Fetch metadata and coordinate-file URLs by ID — experimental (PDB), predicted (AlphaFold), or best-available — with batch partial success and optional coordinate inlining. |
protein_find_similar | Find sequence homologs (RCSB mmseqs2) or fold homologs (Foldseek) from a sequence, PDB ID, or UniProt accession. |
protein_track_ligands | Resolve ligand names/formulas to component IDs, find structures containing a ligand, or map binding-site residues. |
protein_compare_structures | Structurally align 2–10 structures (TM-align / jFATCAT) to a reference or as a full pairwise matrix. |
protein_analyze_collection | Profile the PDB into distributions and trends with server-side facets — counts, histograms, timelines, and cross-tabs. |
protein_get_annotations | Fetch UniProt features and natural variants plus InterPro domain/family memberships with GO terms. |
protein_search_structuresFederated search across experimental (PDB) and predicted (computed-model) structures via RCSB Search v2.
content_type scopes the search to experimental, predicted, or allfacets return a method / organism / release-year breakdown alongside the hits at no extra callprotein_get_structureprotein_get_structureFetch structures with metadata and coordinate-file URLs, resolving across providers by source.
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