ReviewFrontiers in bioengineering and biotechnology2025
Evaluating the advancements in protein language models for encoding strategies in protein function prediction: a comprehensive review.
Review in Frontiers in bioengineering and biotechnology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- KRstereo: Predicting β-Hydroxy Stereochemistry in Polyketides Using Protein Language Models.Journal of chemical information and modeling · 2026Article
- Technical review of artificial intelligence in TCR-T therapy.Journal of the National Cancer Center · 2026Review
- Machine Learning Approaches for Compound-Target Interaction Prediction: A Review.Foods (Basel, Switzerland) · 2026Review
- Accelerating natural product discovery with linked MS-genomics and language/transformer-based models.npj antimicrobials and resistance · 2026Article
- Amino acid composition drives aggregation during peptide synthesis.Nature chemistry · 2026Article
- Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning.Briefings in bioinformatics · 2026Article
- MoCETSE: A mixture-of-convolutional experts and transformer-based model for predicting Gram-negative bacterial secreted effectors.PLoS computational biology · 2026Article
- Protein language models enable accurate viral host range prediction.Scientific reports · 2026Article
- Advancing codon language modeling with synonymous codon constrained masking.Nucleic acids research · 2026Article
- Protein Language Models: Applications and Perspectives.Journal of proteome research · 2026Review
- Modifying inhibitor specificity for homologous enzymes by machine learning.The FEBS journal · 2026Article
- Learning the language of protein-protein interactions.Nature communications · 2026Article
- Sequence Prediction, Structural Modelling and the Challenges of Plasticity in Coiled Coils.Sub-cellular biochemistry · 2026Review
- TXNDC12 and GDF2 as genetically supported plasma proteins associated with knee osteoarthritis: evidence from Mendelian randomization and preliminary biological support.Frontiers in medicine · 2026Article
- Interpretable prediction of nucleic acid-binding proteins using a protein language model.Bioinformatics advances · 2026Article
- Protein Language Models in Virology: A Review of Advances and Applications.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Article
- ALLM-Ab: Active Learning-Driven Antibody Optimization Using Fine-Tuned Protein Language Models.Journal of chemical information and modeling · 2025Article
- Prediction of peptide cleavage sites using protein language models and graph neural networks.Scientific reports · 2025Article
- Application of Protein Structure Encodings and Sequence Embeddings for Transporter Substrate Prediction.Molecules (Basel, Switzerland) · 2025Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein function prediction is crucial in several key areas such as bioinformatics and drug design. With the rapid progress of deep learning technology, applying protein language models has become a research focus. These models utilize the increasing amount of large-scale protein sequence data to deeply mine its intrinsic semantic information, which can effectively improve the accuracy of protein function prediction. This review comprehensively combines the current status of applying the latest protein language models in protein function prediction. It provides an exhaustive performance comparison with traditional prediction methods. Through the in-depth analysis of experimental results, the significant advantages of protein language models in enhancing the accuracy and depth of protein function prediction tasks are fully demonstrated.
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