{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Peng FZ"],"funding":["U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences","U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)"],"pagination":["945-949"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12074982"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["22(5)"],"pubmed_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."],"journal":["Nature methods"],"pubmed_title":["PTM-Mamba: a PTM-aware protein language model with bidirectional gated Mamba blocks."],"pmcid":["PMC12074982"],"funding_grant_id":["1R35GM1555282-01"],"pubmed_authors":["Schussheim B","Wang C","Chatterjee P","Vincoff S","Peng FZ","Chen T"],"additional_accession":[]},"is_claimable":false,"name":"PTM-Mamba: a PTM-aware protein language model with bidirectional gated Mamba blocks.","description":"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.","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 May","modification":"2026-06-02T07:06:43.332Z","creation":"2026-04-15T03:15:26.839Z"},"accession":"S-EPMC12074982","cross_references":{"pubmed":["40211004"],"doi":["10.1038/s41592-025-02656-9"]}}