ai4protein FoldSeek Structural Similarity
Overview
Runs the VenusFactory FoldSeek submit→poll→download pipeline. Coordinates are 1-based inclusive for protect_start / protect_end (masked region kept out of the search query).
Project Tools (VenusFactory2)
| Tool | Args | Returns |
|---|---|---|
| download_foldseek_results_by_pdb_file | pdb_file_path, protect_start, protect_end, optional out_dir |
rich JSON; m8/FASTA under file_info |
| download_rcsb_structure_by_pdb_id | hit PDB ids | fetch neighbors |
| superpose_two_structures | query + hit PDBs | visual compare |
Workflow
- Ensure a local PDB (user upload, AlphaFold, or RCSB).
- Choose protect region (catalytic site / epitope) or pass a wide range if no mask needed — both start and end are required by the tool.
- Call
download_foldseek_results_by_pdb_file; wait for submit-poll to finish (network latency expected). - Parse hits from
content_preview/ saved m8; fetch interesting hits via RCSB; optional superpose.
When NOT to use
- Sequence identity / remote homologs without structure →
protein_sequence_similarity_search - Align many sequences →
clustalo_msa
Common mistakes
- Using 0-based residue indices.
- Confusing FoldSeek with sequence BLAST tools.
- Ignoring timeouts on the webserver queue — report
status:errorsuggestion to user.