foldseek-structural-search

To perform a protein structural homology search, you submit a physical 3D coordinate file with a .pdb, .cif, or .mmcif extension. The tool queries validated Foldseek databases and returns a Markdown summary with top structural matches.

You cannot find distant homologous proteins using sequence-only search because this tool requires physical 3D structure files. It specifically halts if the input is sequence or ID-based, enforcing strict validation for structural alignment tasks.

Available Foldseek databases for 3D structural alignment include afdb50, pdb100, and cath50. The tool enforces an allowed database list and stops execution if you request an unsupported database for your structural similarity search.

Structural search results are written as both a human-readable Markdown table for quick review and a full JSON payload for deeper analysis. These outputs are written directly to disk after querying the Foldseek API using 3diaa mode metrics.

The Foldseek API search supports MMCIF coordinate files, accepting .mmcif, .cif, and .pdb extensions. It applies strict input validation to ensure only physical 3D coordinate files are submitted for structural similarity matching.

Your structural homology search fails to start if the input file is sequence or ID-based instead of a validated .pdb, .cif, or .mmcif coordinate file, or if you request a database outside the allowed list.