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MCP live MCP 2026-07-28 http ext: skills

protein-mcp-server

cyanheads/protein-mcp-server

Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models.

Watch this dependency Share evidence report
Uptime
100.0%
5 direct probes · 30d
Response
1900ms
last probe
Tools
7
callable
Resources
1
readable
Prompts
0
available
Primary URL
https://protein.caseyjhand.com/mcp
Score: 100/100
Handshake verified by our own probe.
pass Answers the MCP handshake 50/50
The handshake and the list calls succeeded on the primary URL.
pass Lists tools, resources or prompts 30/30
7 tools, 1 resources, 0 prompts returned.
pass 3 or more catalogue items 10/10
8 items in total; 3 or more earns these points.
pass Describes itself 10/10
100 characters; more than 30 earns these points.

Tools · 7

protein_search_structures

Search experimental (PDB) and predicted (computed-model) protein structures by free text, protein sequence (triggers an mmseqs2 similarity search), and/or organism, method, resolution, and bound-ligan…

protein_get_structure

Fetch structures with metadata and coordinate-file URLs. source "experimental" takes PDB entry IDs, and also resolves the computed-model IDs protein_search_structures returns (AF_*/MA_*), which come b…

protein_find_similar

Find structurally or evolutionarily related proteins. by:"sequence" runs an RCSB mmseqs2 sequence-similarity search (synchronous; experimental PDB entries only — protein_search_structures with a seque…

protein_track_ligands

Ligand discovery and binding-site analysis across the PDB. mode "find_ligand" resolves a name or formula to chemical component IDs with metadata (formula, weight, SMILES), ranked by deposition frequen…

protein_compare_structures

Structurally align multiple structures (up to the configured batch cap; structures past it are returned in ignored) via the RCSB Structural Comparison service (TM-align / jFATCAT). reference:"first" a…

protein_analyze_collection

Profile the PDB into distributions and trends over an optional scoping query: counts by method, organism, or polymer composition; resolution and molecular-weight histograms; release-year timelines; an…

protein_get_annotations

Sequence and functional annotation for a protein: UniProt positional features (domains, binding and active sites, PTMs including cross-links and lipidation, topology, DNA binding, processing products …

Resources · 1

protein-guide

Identifier chains and gates for the protein_* tools - which ID each tool takes (PDB entry, polymer entity, RCSB computed model, AlphaFold entry, UniProt accession or isoform, ligand component), author…

skill://protein-guide/SKILL.md

Skills · 1

protein-guide

Identifier chains and gates for the protein_* tools - which ID each tool takes (PDB entry, polymer entity, RCSB computed model, AlphaFold entry, UniProt accession or isoform, ligand component), author…

skill://protein-guide/SKILL.md
1 file

How to use

Claude Desktop or claude.ai: add a custom connector (Customize → Connectors; on Team and Enterprise plans an owner adds it under Organization settings → Connectors) with this server URL: https://protein.caseyjhand.com/mcp

Cursor or Cline: add to your MCP config:

{
  "mcpServers": {
    "protein-mcp-server": {
      "url": "https://protein.caseyjhand.com/mcp",
      "transport": "http"
    }
  }
}