DPFunc: accurately predicting protein function via deep learning with domain-guided structure information

Wenkang Wang, Yunyan Shuai, Min Zeng, Wei Fan and Min Li ()
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Wenkang Wang: Central South University
Yunyan Shuai: Central South University
Min Zeng: Central South University
Wei Fan: University of Oxford
Min Li: Central South University

Nature Communications, 2025, vol. 16, issue 1, 1-13

Abstract: Abstract Computational methods for predicting protein function are of great significance in understanding biological mechanisms and treating complex diseases. However, existing computational approaches of protein function prediction lack interpretability, making it difficult to understand the relations between protein structures and functions. In this study, we propose a deep learning-based solution, named DPFunc, for accurate protein function prediction with domain-guided structure information. DPFunc can detect significant regions in protein structures and accurately predict corresponding functions under the guidance of domain information. It outperforms current state-of-the-art methods and achieves a significant improvement over existing structure-based methods. Detailed analyses demonstrate that the guidance of domain information contributes to DPFunc for protein function prediction, enabling our method to detect key residues or regions in protein structures, which are closely related to their functions. In summary, DPFunc serves as an effective tool for large-scale protein function prediction, which pushes the border of protein understanding in biological systems.

Date: 2025
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DOI: 10.1038/s41467-024-54816-8

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