Peking University team builds AI tool ContactSeek using AlphaFold3 for precise gene editing

A team from Peking University and East China Normal University published a paper in Nature, introducing ContactSeek, an AI framework based on AlphaFold3's contact probability for precise base editing. The researchers combined AlphaFold3's predictions with high-throughput off-target data to identify key amino acids affecting editing accuracy. By engineering these sites, they significantly improved precision while reducing unwanted edits. The framework can detect tiny structural changes caused by single base mismatches. The team has already found new Cas9 variants that maintain high on-target activity with fewer off-target effects, offering a new approach for designing safer gene therapy tools.