Across 40 PTM-site benchmarks, ProtSyntax improved mean MCC and AP by 12.7% and 10.7%, respectively, relative to the best-performing baselines, and provides an interpretable framework for decoding PTM regulation across the proteome.
TaHL-PTM (Target-Hooked Low-rank adaptation for PTM prediction), a novel framework that integrates target-hooked tokenization with site-directed discriminative LoRA fine-tuning that generalizes across models with different pretraining tokenization schemes is proposed.
Bhawana Prasain, Pawel Pratyush, Stefan Schulze et al.· bioRxiv· 0 citations
This work proposes an anchor-guided rectified flow matching framework for multi-type PTM site prediction from protein language model embeddings and suggests that multi-type PTM prediction can be modeled within a single shared framework by combining residue-background anchors with modification-conditioned offset feature...
PlantPTM, an integrated deep learning framework for predicting nine PTM types in plants demonstrates robust generalizability across a wide range of PTM types and plant species and achieves state-of-the-art performance.
ProtLingo, an efficient PLM framework that augments a pretrained single-sequence backbone with conditional local memory and sparse expert routing, achieves competitive performance with a 150M-scale backbone, including strong parameter efficiency on mutation-effect prediction and preserved long-range structural represen...
Ming-Rui Li, Si-Xian Shen, Min-Zhang Li et al.· 0 citations
Dyna-MO PTM brings together 1,079 AlphaFold 3-seeded systems covering lysine acetylation, lysine and arginine monomethylation, and serine, threonine and tyrosine phosphorylation to filter PTM contexts, reproduce descriptors, prioritise longer simulations and evaluate trajectory-analysis or generative methods.
Applications to thioredoxins, visual opsins, and Tara Oceans environmental diatom cold-shock proteins show that PLMView can move from interpretable residue-level determinants in well-studied protein families to large-scale environmental functional discovery, linking molecular specialization to ecological distribution a...
