AlphaFold

The AlphaFold MCP Server provides comprehensive access to DeepMind's AlphaFold Protein Structure Database through 22 specialized tools covering structure retrieval, confidence analysis, batch processing, and comparative analysis. Built by Augmented Nature, it integrates directly with the AlphaFold API to enable protein structure searches by UniProt ID or organism, download structures in multiple formats (PDB, CIF, mmCIF), analyze per-residue confidence scores, and export data for visualization tools like PyMOL and ChimeraX. The server is particularly valuable for structural biology research, protein analysis workflows, and bioinformatics applications where users need programmatic access to high-quality protein structure predictions without manually navigating the AlphaFold database interface.