ArticleNature methods2025
PTM-Mamba: a PTM-aware protein language model with bidirectional gated Mamba blocks.
Article in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- A trimodal protein language model enables advanced protein searches.Nature biotechnology · 2026Article
- Artificial intelligence in plant salt stress research: from predictive models to multi-omics integration.Journal of experimental botany · 2026Review
- SPAID: a comprehensive database for disease-specific autoantigens in autoimmune disorders.Advanced biotechnology · 2026Article
- amyloid-predict and LLPS-predict: Predicting phase separation propensities in the intrinsically disordered proteome.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Peptide binders designed directly from protein sequences.Nature biotechnology · 2026Article
- Generalist biological artificial intelligence in modeling the language of life.Nature biotechnology · 2026Review
- Target sequence-conditioned design of peptide binders using masked language modeling.Nature biotechnology · 2026Article
- ProteomeLM: A proteome-scale language model enables accurate and rapid prediction of protein-protein interactions and gene essentiality across taxa.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Learning the PTM code through a coarse-to-fine mechanism-aware framework.Nature communications · 2026Article
- Protein foundation models: a comprehensive survey.Science China. Life sciences · 2026Review
- Post-translational modifications of silk proteins.RSC chemical biology · 2026Review
- Functional protein design and enhancement with ontology reinforcement iteration.Nature communications · 2026Article
- Leveraging learned representations and multitask learning for lysine methylation site discovery.Scientific reports · 2026Article
- Protein Language Models: Applications and Perspectives.Journal of proteome research · 2026Review
- PMADS: an integrated database of curated and proteomics-inferred associations between protein post-translational modifications and drug sensitivity.Nucleic acids research · 2026Article
- Leveraging AI-driven predictors of enzyme pH optima to unravel microbial adaptation to environmental pH.Frontiers in microbiology · 2026Article
- Application and Prospects of Large Language Models in Small-Molecule Drug Discovery.Analytical chemistry · 2025Review
- Article
- A deep learning framework for lysine 2-hydroxyisobutyrylation site prediction using evolutionary feature representation.Scientific reports · 2025Article
- Prediction of liquid-liquid phase separation proteins based on protein language model.Briefings in bioinformatics · 2025Article
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6 authors.
Funding
Abstract
Current protein language models (LMs) accurately encode protein properties but have yet to represent post-translational modifications (PTMs), which are crucial for proteomic diversity and influence protein structure, function and interactions. To address this gap, we develop PTM-Mamba, a PTM-aware protein LM that integrates PTM tokens using bidirectional Mamba blocks fused with ESM-2 protein LM embeddings via a newly developed gating mechanism. PTM-Mamba uniquely models both wild-type and PTM sequences, enabling downstream tasks such as disease association and druggability prediction, PTM effect prediction on protein-protein interactions and zero-shot PTM discovery. In total, our work establishes PTM-Mamba as a foundational tool for PTM-aware protein modeling and design.
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