Auto-Research Agent on MSA Organization to Improve Protein-Protein Complex Structure Prediction
Protein-complex structure prediction with AlphaFold 3 depends on MSA content, depth, and cross-chain pairing. Current pipelines apply uniform recipes, typically maximizing depth and pairing by species, yet even whether cross-chain pairing helps AF3 remains contested. We show that the value of both depth and pairing is...
Zi-Lu Zhang, Jing Bao, Li-Feng Qiao et al.
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