2024/10/02 by Jiaqing Xie, Tianfan Fu, Xie, Jiaqing +1 · 1 citation
Biochemistry, Genetics and Molecular Biology · #Artificial Intelligence (cs.AI) #FOS: Biological sciences #FOS: Computer and information sciences #Genetics, Bioinformatics, and Biomedical Research #Machine Learning (cs.LG) #Machine Learning in Bioinformatics #Quantitative Methods (q-bio.QM) #vaccines and immunoinformatics approaches
paper · pdf · doi:10.48550/arxiv.2410.02023
openalex publication_date 2024/10/02 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Deep learning has deeply influenced protein science, enabling breakthroughs in predicting protein properties, higher-order structures, and molecular interactions. This paper introduces DeepProtein, a comprehensive and user-friendly deep learning library tailored for protein-related tasks. It enables researchers to seamlessly address protein data with cutting-edge deep learning models. To assess model performance, we establish a benchmark evaluating different deep learning architectures across multiple protein-related tasks, including protein function prediction, subcellular localization prediction, protein-protein interaction prediction, and protein structure prediction. Furthermore, we introduce DeepProt-T5, a series of fine-tuned Prot-T5-based models that achieve state-of-the-art performance on four benchmark tasks, while demonstrating competitive results on six of others. Comprehensive documentation and tutorials are available which could ensure accessibility and support reproducibility. Built upon the widely used drug discovery library DeepPurpose, DeepProtein is publicly available at https://github.com/jiaqingxie/DeepProtein.