foldseeklisted

# Foldseek Structure Search ## Prerequisites | Requirement | Minimum | Recommended | |-------------|---------|-------------| | Python | 3.8+ | 3.10 | | RAM | 8GB | 16GB | | Disk | 10GB | 50GB (for local databases) | ## How to run **Note**: Foldseek can run locally or via web server. No GPU required. ### Option 1: Web Server (Quick; rate-limited, use sparingly) ```bash # Upload structure to web server curl -X POST "https://search.foldseek.com/api/ticket" \ -F "q=@query.pdb" \ -F "database[]=afdb50" \ -F "database[]=pdb100" ``` ### Option 2: Local installation ```bash # Install Foldseek conda install -c conda-forge -c bioconda foldseek # Search PDB foldseek easy-search query.pdb /path/to/pdb100 results.m8 tmp/ # Search AlphaFold DB foldseek easy-search query.pdb /path/to/afdb50 results.m8 tmp/ ``` ### Option 3: Python API ```python import subprocess import pandas as pd def foldseek_search(query_pdb, database, output="results.m8"): """Run Foldseek search.""" subprocess.run([ "foldseek", "easy-search", query_pdb, database, output, "tmp/", "--format-output", "query,target,pident,alnlen,evalue,bits" ]) return pd.read_csv(output, sep="\t", names=["query", "target", "pident", "alnlen", "evalue", "bits"]) ``` ## Key parameters | Parameter | Default | Description | |-----------|---------|-------------| | `--min-seq-id` | 0.0 | Minimum sequence identity | | `-e` | 0.001 | E-value threshold | | `--alignment-