AlphaPulldown

AlphaPulldown is a computational pipeline that leverages AlphaFold-Multimer to screen and predict protein-protein interactions (PPIs) systematically. It is especially useful for exploring large-scale interactomes, or validating potential protein partners.

AlphaPulldown automates the process of:

1. Pairing proteins (from a list or dataset)
2. Running AlphaFold-Multimer predictions for each pair
3. Scoring and ranking the results to identify likely binding partners

It's inspired by experimental pulldown assays but done entirely in silico.

Key Features:

• High-throughput interaction screening
• Supports pairwise and multi-chain interaction predictions
• Generates confidence metrics like pLDDT and interface scores (e.g., ipTM)
• Can be integrated into drug discovery or systems biology workflows

Applications

• Mapping protein interaction networks
• Identifying binding partners for uncharacterized proteins
• Validating interactions in silico before experimental testing
• Structural modeling of protein complexes

Advantages

• Efficient for large datasets (genome-wide or proteome-wide)
• Based on AlphaFold-Multimer, offering high structural accuracy
• Reduces experimental cost and time for interaction discovery

Limitations

• Accuracy depends on AlphaFold-Multimer’s performance, which may be lower for transient or weak interactions
• Cannot directly capture dynamic or context-dependent interactions
• May predict false positives, requiring validation