foldseek-structural-similarity

name	foldseek_structural_similarity
description	FoldSeek structural similarity search against PDB with optional protected-region masking. Use when the user has a PDB and wants fold-level homologs, structural neighbors, or to protect an active site while searching. Do NOT use for sequence BLAST/MMseqs2 (protein_sequence_similarity_search) or MSA (clustalo_msa).
license	Apache-2.0
metadata	{"version":"1.0","skill-author":"VenusFactory2"}

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

1. Ensure a local PDB (user upload, AlphaFold, or RCSB).
2. Choose protect region (catalytic site / epitope) or pass a wide range if no mask needed — both start and end are required by the tool.
3. Call download_foldseek_results_by_pdb_file; wait for submit-poll to finish (network latency expected).
4. 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:error suggestion to user.