protein_compare_structures

MCP tool from Protein MCP Server by cyanheads

Structurally align multiple structures (TM-align / jFATCAT) to a reference or as a full pairwise matrix.

How to use it

Project documentation lists protein_compare_structures for the Protein MCP Server MCP server. Add the server to your MCP client (Claude Desktop, Cursor, Windsurf and others), then check which tools your installed version makes available. Tool availability can depend on configuration and credentials. A server handshake does not verify this tool’s behavior. See the full listing for setup details.

Install Protein MCP Server

$bunx @cyanheads/protein-mcp-server@latest

FULL PROTEIN MCP SERVER LISTING

Other tools in Protein MCP Server (6)

protein_analyze_collection

Profile the PDB into distributions and trends with server-side facets — counts, histograms, timelines, and cross-tabs.

protein_find_similar

Find sequence homologs (RCSB mmseqs2) or fold homologs (Foldseek) from a sequence, PDB ID, or UniProt accession.

protein_get_annotations

Fetch UniProt features and natural variants plus InterPro domain/family memberships with GO terms.

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_search_structures

Search experimental and predicted structures by free text, sequence, or organism/method/resolution filters, with optional facet breakdowns.

protein_track_ligands

Resolve ligand names/formulas to component IDs, find structures containing a ligand, or map binding-site residues.