Protein Mcp Server
by cyanheadscommunityv1.0.3
4
This MCP server provides programmatic access to 3D protein structural data from various sources, featuring multi-provider orchestration and comprehensive structural analysis tools.
From the registry: MCP Server for 3D protein structural data retrieval & analysis from RCSB PDB, PDBe, and UniProt.
Install & configure
Prerequisites
- required
Install in your client
Paste into the AI you're chatting with — it will figure out the rest
Please install the `protein-mcp-server` MCP server into my current AI client (that's you).
Required prerequisites (do these first if not already done):
- **Bun v1.2.0+** — Install Bun runtime (https://bun.sh/)
Canonical MCP server config (stdio transport):
- command: `bunx`
- args: ["protein-mcp-server@latest"]
- optional environment variables:
- `MCP_LOG_LEVEL`: Log level: info, debug, warn, error (example: `info`)
- `MCP_TRANSPORT_TYPE`: Transport: stdio or http (example: `stdio`)
Note: 3D protein structural data from RCSB PDB, PDBe, UniProt. No API keys required. Also has public hosted instance at https://pubchem.caseyjhand.com/mcp (wrong link in README - this is protein server).
Add this MCP server to my current client's config in the correct format for you. If you need secrets or credentials I haven't provided, ASK me — do not invent values or leave raw placeholders. After adding it, tell me how to verify the server is connected.Note: 3D protein structural data from RCSB PDB, PDBe, UniProt. No API keys required. Also has public hosted instance at https://pubchem.caseyjhand.com/mcp (wrong link in README - this is protein server).
Tools (6)
protein_search_structures
Searches for protein structures using keywords, filters, pagination, and sorting.
protein_get_structure
Fetches one or more protein structures by their PDB IDs, returning either full data or concise summaries.
protein_find_similar
Finds proteins with similar sequence or structure.
protein_track_ligands
Finds protein structures containing specific ligands, cofactors, or drugs.
protein_compare_structures
Performs a detailed side-by-side comparison of 2-10 protein structures.
protein_analyze_collection
Performs statistical analysis on the protein structure database.
Environment variables
MCP_TRANSPORT_TYPErequiredThe transport to use: `stdio` or `http`.MCP_HTTP_PORTrequiredThe port for the HTTP server.MCP_AUTH_MODErequiredAuthentication mode: `none`, `jwt`, or `oauth`.STORAGE_PROVIDER_TYPErequiredStorage backend: `in-memory`, `filesystem`, `supabase`, `cloudflare-kv`, `r2`.PROTEIN_PRIMARY_PROVIDERrequiredThe primary data source for protein data.OTEL_ENABLEDrequiredSet to `true` to enable OpenTelemetry.LOG_LEVELrequiredThe minimum level for logging.Packages
protein-mcp-server
npmv1.0.3transport: stdio
protein-mcp-server
npmv1.0.3transport: streamable-http
Details
- Language
- TypeScript
- License
- Apache-2.0
- Released
- Oct 3, 2025
- Last commit
- Jun 24, 2026
- Registry name
- io.github.cyanheads/protein-mcp-server
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