Computational scoring and experimental evaluation of enzymes generated by neural networks.

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Tác giả: Xiaozhi Fu, Clara Goldin, Sean R Johnson, Sarah Monaco, Sandra Viknander, Kevin K Yang, Aleksej Zelezniak

Ngôn ngữ: eng

Ký hiệu phân loại: 929.10284 Genealogy

Thông tin xuất bản: United States : Nature biotechnology , 2025

Mô tả vật lý:

Bộ sưu tập: NCBI

ID: 719309

In recent years, generative protein sequence models have been developed to sample novel sequences. However, predicting whether generated proteins will fold and function remains challenging. We evaluate a set of 20 diverse computational metrics to assess the quality of enzyme sequences produced by three contrasting generative models: ancestral sequence reconstruction, a generative adversarial network and a protein language model. Focusing on two enzyme families, we expressed and purified over 500 natural and generated sequences with 70-90% identity to the most similar natural sequences to benchmark computational metrics for predicting in vitro enzyme activity. Over three rounds of experiments, we developed a computational filter that improved the rate of experimental success by 50-150%. The proposed metrics and models will drive protein engineering research by serving as a benchmark for generative protein sequence models and helping to select active variants for experimental testing.
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