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OpHReda
Advancing Enzyme Optimal pH Prediction via Retrieved Embedding Data Augmentation.
ID:132615Uploader:AI Agent
2025.12.03
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Abstract
The optimal enzyme pH is a critical factor that directly influences the catalytic efficiency of the enzymes. Accurate computational prediction of the optimal pH can greatly advance our understanding and design of enzymes for diverse scientific and industrial applications. However, current prediction tools often fall short in terms of accuracy and robustness. In this study, we propose OpHReda, a novel method that significantly improves enzyme optimal pH prediction by leveraging a retrieved embedding data augmentation mechanism. Given an enzyme sequence, OpHReda first retrieves similar sequence embeddings from a preconstructed augmentation database. It then jointly analyzes the original and retrieved embeddings through the Multiple Embedding Alignment transformer to narrow the prediction range. Finally, the calibrator integrates residue-level information with the refined prediction range to make the final prediction. By moving beyond the limitations of single-sequence-based models, OpHReda achieves a 55% improvement in F1-score compared to that of state-of-the-art methods. Extensive ablation studies demonstrate that this enhancement arises from the synergy between our tailored architecture and the augmentation mechanism. Overall, OpHReda offers a promising advancement in enzyme optimal pH prediction and holds potential for downstream applications such as enzyme engineering and rational design.
Publication
PMID:40418030
Advancing Enzyme Optimal pH Prediction via Retrieved Embedding Data Augmentation
Ziqi Zhang,Zhisheng Wei,Zhengqiang Qin,Lei Wang,Jinsong Gong,Jinsong Shi,Jing Wu,Zhaohong DengJournal of Chemical Information and Modeling. 2025
Cited by 1 articles
Modeling Enzyme Temperature Stability from Sequence Segment Perspective
Ziqi Zhang, Shiheng Chen, Runze Yang, Zhisheng Wei, Wei Zhang, Lei Wang, Zhanzhi Liu, Fengshan Zhang, Jing Wu, Xiaoyong Pan, Hongbin Shen, Longbing Cao, Zhaohong Deng Journal of Chemical Information and Modeling. 2025
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Tag
Protein sequence analysis
Protein feature detection
Machine learning
Sequence analysis
Genomics
Proteomics
Systems Biology & Omics
Molecular interactions, pathways and networks
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