ArticleBioinformatics (Oxford, England)2025
DeepProtein: deep learning library and benchmark for protein sequence learning.
Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- PeptiVerse: A unified platform for therapeutic peptide property prediction.Nature communications · 2026Article
- Augmented prediction of multi-species protein-RNA interactions using evolutionary conservation of RNA-binding proteins.Nature communications · 2026Article
- Predicting SJournal of chemical theory and computation · 2026Article
- PeptiVerse: A Unified Platform for Therapeutic Peptide Property Prediction.bioRxiv : the preprint server for biology · 2026Article
- Locality-aware pooling enhances protein language model performance across varied applications.Bioinformatics (Oxford, England) · 2025Article
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Authors and funding
3 authors.
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Abstract
motivationDeep learning has deeply influenced protein science, enabling breakthroughs in predicting protein properties, higher-order structures, and molecular interactions.
resultsThis article 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 that evaluates 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. AVAILABILITY AND IMPLEMENTATION: Built upon the widely used drug discovery library DeepPurpose, DeepProtein is publicly available at https://github.com/jiaqingxie/DeepProtein.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.