ProtAlign-ARG: antibiotic resistance gene characterization integrating protein language models and alignment-based scoring by Shafayat Ahmed, Muhit Islam Emon, Nazifa Ahmed Moumi, Lifu Huang, Dawei Zhou, Peter Vikesland, Amy Pruden, Liqing Zhang

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Semantical and geometrical protein encoding toward enhanced bioactivity and thermostability by Yang Tan, Bingxin Zhou, Lirong Zheng, Guisheng Fan, Liang Hong

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Optimizing enzyme thermostability by combining multiple mutations using protein language model by Jiahao Bian, Pan Tan, Ting Nie, Liang Hong, Guang‐Yu Yang

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OPUS-BFactor: Predicting Protein B-Factor with Sequence and Structure Information by Yulu Yang, Ying Lv, Zhenwei Luo, Qinghua Wang, Gang Xu, Jianpeng Ma

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UniAMP: enhancing AMP prediction using deep neural networks with inferred information of peptides by Zixin Chen, Chengming Ji, Wenwen Xu, Jianfeng Gao, Ji Huang, Huanliang Xu, Guoliang Qian, Junxian Huang

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ConoGPT: Fine-Tuning a Protein Language Model by Incorporating Disulfide Bond Information for Conotoxin Sequence Generation by Guohui Zhao, Cheng Ge, Wenzheng Han, Rilei Yu, Hao Liu

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The Accurate Prediction of Antibody Deamidations by Combining High-Throughput Automated Peptide Mapping and Protein Language Model-Based Deep Learning by Ben Niu, Benjamin Lee, Lili Wang, Wen Chen, Jeffrey Johnson

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Bio-Inspired Mamba for Antibody–Antigen Interaction Prediction by Xuan Liu, Haitao Fu, Yuqing Yang, Jian Zhang

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Integration of pre-trained protein language models with equivariant graph neural networks for peptide toxicity prediction by Shihu Jiao, Xiucai Ye, Tetsuya Sakurai, Quan Zou, Wu Han, Chao Zhan

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Highly accurate prophage island detection with PIDE by Hongyan Gao, Bowen Li, Zihan Guo, Lei Zheng, Junnan Chen, Guanxiang Liang

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Advancing the accuracy of clathrin protein prediction through multi-source protein language models by Watshara Shoombuatong, Nalini Schaduangrat, Pakpoom Mookdarsanit, Jaru Nikom, Lawankorn Mookdarsanit

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BIDpred: unraveling B cell Immunodominance hierarchical pattern using statistical feature discovery and deep learning prediction by Sungjin Choi, Dongsup Kim

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Do domain-specific protein language models outperform general models on immunology-related tasks? by Nicolas Deutschmann, Aurelien Pelissier, Anna Weber, Shuaijun Gao, Jasmina Bogojeska, María Rodríguez Martínez

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Enhancing the reverse transcriptase function in Taq polymerase via AI-driven multiparametric rational design by Yulia E. Tomilova, Nikolay E. Russkikh, Igor M. Yi, Elizaveta V. Shaburova, Viktor N. Tomilov, Galina B. Pyrinova, Svetlana O. Brezhneva, Olga S. Tikhonyuk, Nadezhda S. Gololobova, Dmitriy V. Popichenko, Maxim O. Arkhipov, Leonid O. Bryzgalov, Evgeniy V. Brenner, Anastasia A. Artyukh, Dmitry N. Shtokalo, Dmitry N. Shtokalo, Dmitry N. Shtokalo, Denis V. Antonets, Mikhail K. Ivanov, Mikhail K. Ivanov

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Accurate prediction of virulence factors using pre-train protein language model and ensemble learning by Guanghui Li, Jian Zhou, Jiawei Luo, Cheng Liang

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PLM-ATG: Identification of Autophagy Proteins by Integrating Protein Language Model Embeddings with PSSM-Based Features by Yangying Wang, Chunhua Wang

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iNClassSec-ESM: Discovering potential non-classical secreted proteins through a novel protein language model by Yizhou Shao, Taigang Liu

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CPL‐Diff: A Diffusion Model for De Novo Design of Functional Peptide Sequences with Fixed Length by Zhenjie Luo, Aoyun Geng, Leyi Wei, Quan Zou, Feifei Cui, Zilong Zhang

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The Historical Evolution and Significance of Multiple Sequence Alignment in Molecular Structure and Function Prediction by Chenyue Zhang, Qinxin Wang, Yiyang Li, Anqi Teng, Gang Hu, Qiqige Wuyun, Wei Zheng

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MTPrompt-PTM: A Multi-Task Method for Post-Translational Modification Prediction Using Prompt Tuning on a Structure-Aware Protein Language Model by Ye Han, Fei He, Qing Shao, Duolin Wang, Dong Xu

Subjects: “…structure-aware protein language model (S-PLM)…”
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