foldseek

# 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-type` | 2 | 0=3Di, 1=TM, 2=3Di+AA |
| `--max-seqs` | 300 | Max hits to pass through prefilter; reducing this affects sensitivity |

## Databases

| Database | Description | Size |
|----------|-------------|------|
| `pdb100` | PDB clustered at 100% | ~200K structures |
| `afdb50` | AlphaFold DB at 50% | ~67M structures |
| `swissprot` | SwissProt structures | ~500K structures |
| `cath50` | CATH domains | ~50K domains |

## Output format

```
# results.m8 (tabular)
query   target          pident  alnlen  evalue  bits
query   1abc_A          85.2    120     1e-45   180.5
query   2def_B          72.1    115     1e-32   145.2
```

## Sample output

### Successful run
```
$ foldseek easy-search query.pdb pdb100 results.m8 tmp/
[INFO] Loading database: pdb100 (194,527 entries)
[INFO] Searching...
[INFO] Found 127 hits

Top 5 hits:
1. 1abc_A - 85.2% identity, E=1e-45
2. 2def_B - 72.1% identity, E=1e-32
3. 3ghi_C - 68.5% identity, E=1e-28
4. 4jkl_A - 55.3% identity, E=1e-18
5. 5mno_B - 42.1% identity, E=1e-10
```

## Decision tree

```
Should I use Foldseek?
│
├─ What are you searching?
│  ├─ By 3D structure → Foldseek ✓
│  ├─ By sequence → Use BLAST (uniprot skill)
│  └─ Both → Run both, compare results
│
└─ What do you need?
   ├─ Find structural homologs → Foldseek ✓
   ├─ Remote homolog detection → Foldseek ✓
   ├─ Structural clustering → Foldseek ✓
   └─ Functional annotation → Cross-reference with UniProt
```

## Common use cases

### Find similar designs
```bash
# Compare your design to PDB
foldseek easy-search design.pdb pdb100 similar_natural.m8 tmp/
```

### Novelty check
```bash
# Ensure design is novel (low similarity to known)
foldseek easy-search design.pdb afdb50 novelty.m8 tmp/

# Novel if: top hit identity < 30%
```

### Scaffold search
```bash
# Find scaffolds for motif grafting
foldseek easy-search motif.pdb pdb100 scaffolds.m8 tmp/ \
  --min-seq-id 0.0 -e 10
```

---

## Verify

```bash
wc -l results.m8  # Number of hits
```

---

## Troubleshooting

**No hits**: Lower e-value threshold, try larger database
**Too many hits**: Increase min-seq-id threshold
**Slow search**: Use smaller database

### Error interpretation

| Error | Cause | Fix |
|-------|-------|-----|
| `Database not found` | Wrong path | Check database location |
| `Invalid PDB` | Malformed structure | Validate PDB format |
| `Out of memory` | Large database | Use more RAM or web server |

---

**Next**: Download hits with `pdb` skill → use for scaffold design.