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Herein, we provide a detailed examination of alphafold3’s capabilities, emphasizing its applications across diverse biological fields and its effectiveness in complex biological systems. Using a curated collection of 254 available protein targets with both unbound and bound structures, we first demonstrate that alphafold confidence measures (plddt) can be repurposed for estimating protein flexibility and docking accuracy for multimers. Accurate afinity ranking of small molecules is pivotal for drug discovery

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To probe alphafold3’s (af3) capabilities and limitations, we tested af3’s ability to capture the fine details and interplay between antibody structure prediction and antigen docking accuracy. It could revolutionize drug discovery and protein engineering, marking a major step towards comprehensive, automated protein structure prediction.