Peking University Team and Collaborators Publish ContactSeek in Nature, Using AlphaFold3 Contact Probabilities to Improve Base-Editing Specificity

Yi Chengqi's group at Peking University and collaborators published a study in Nature describing ContactSeek, an AI framework based on AlphaFold3 contact probabilities that systematically identifies amino acid residues determining editing specificity in base editors. The work combined AlphaFold3-predicted contact probabilities with off-target editing data from high-throughput sequencing, then engineered Cas proteins and deaminases accordingly, markedly improving editing specificity and establishing a new paradigm for precision design of gene-editing tools.