ArticleGenome biology2024
AnnoPRO: a strategy for protein function annotation based on multi-scale protein representation and a hybrid deep learning of dual-path encoding.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Out-of-distribution generalization enhances protein function annotation for low-homology sequences.Briefings in bioinformatics · 2026Article
- Artificial Intelligence Powers Protein Functional Annotation.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Evaluating network-based algorithms for protein function prediction using plant protein-protein interaction networks.BMC plant biology · 2026Article
- Evolutionary profile enhancement improves protein function annotation for remote homologs.bioRxiv : the preprint server for biology · 2026Article
- PlasticEnz: An integrated database and screening tool combining homology and machine learning to identify plastic-degrading enzymes in meta-omics datasets.PLoS computational biology · 2026Article
- Acidification by nitrogen metabolism triggers extracellular biopolymer production in an oleaginous yeast.Applied and environmental microbiology · 2025Article
- Neurodegeneration Through the Lens of Bioinformatics Approaches: Computational Mechanisms of Protein Misfolding.International journal of molecular sciences · 2025Review
- Interpretation of RNA Universe and Coding Potential Using IntRNA.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- LocPro: A deep learning-based prediction of protein subcellular localization for promoting multi-directional pharmaceutical research.Journal of pharmaceutical analysis · 2025Article
- EZpred: improving deep learning-based enzyme function prediction using unlabeled sequence homologs.bioRxiv : the preprint server for biology · 2025Article
- MKFGO: integrating multi-source knowledge fusion with pretrained language model for high-accuracy protein function prediction.Briefings in bioinformatics · 2025Article
- Review
- Learning maximally spanning representations improves protein function annotation.bioRxiv : the preprint server for biology · 2025Article
- Machine Learning for Protein Function Prediction.Methods in molecular biology (Clifton, N.J.) · 2025Review
- FAPM: functional annotation of proteins using multimodal models beyond structural modeling.Bioinformatics (Oxford, England) · 2024Article
- Deep learning-based design and experimental validation of a medicine-like human antibody library.Briefings in bioinformatics · 2024Article
- Review
- A large-scale assessment of sequence database search tools for homology-based protein function prediction.Briefings in bioinformatics · 2024Article
- FERREG: ferroptosis-based regulation of disease occurrence, progression and therapeutic response.Briefings in bioinformatics · 2024Article
- AnnoPRO: a strategy for protein function annotation based on multi-scale protein representation and a hybrid deep learning of dual-path encoding.Genome biology · 2024Article
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Authors and funding
18 authors.
Funding
Abstract
Protein function annotation has been one of the longstanding issues in biological sciences, and various computational methods have been developed. However, the existing methods suffer from a serious long-tail problem, with a large number of GO families containing few annotated proteins. Herein, an innovative strategy named AnnoPRO was therefore constructed by enabling sequence-based multi-scale protein representation, dual-path protein encoding using pre-training, and function annotation by long short-term memory-based decoding. A variety of case studies based on different benchmarks were conducted, which confirmed the superior performance of AnnoPRO among available methods. Source code and models have been made freely available at: https://github.com/idrblab/AnnoPRO and https://zenodo.org/records/10012272.
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