Detection of circular permutations by Protein Language Models by Yue Hu, Bin Huang, Chun Zi Zang, Jia Jie Xu

Subjects: “…Circular Permutation； Protein Language Models； Protein Structure Alignment…”
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Benchmarking protein language models for protein crystallization by Raghvendra Mall, Rahul Kaushik, Zachary A. Martinez, Matt W. Thomson, Filippo Castiglione

Subjects: “…Open protein language models (PLMs)…”
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T-cell receptor binding prediction: A machine learning revolution by Anna Weber, Aurélien Pélissier, María Rodríguez Martínez

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ParaAntiProt provides paratope prediction using antibody and protein language models by Mahmood Kalemati, Alireza Noroozi, Aref Shahbakhsh, Somayyeh Koohi

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Ion channel classification through machine learning and protein language model embeddings by Ghazikhani Hamed, Butler Gregory

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EquiRank: Improved protein-protein interface quality estimation using protein language-model-informed equivariant graph neural networks by Md Hossain Shuvo, Debswapna Bhattacharya

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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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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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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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Protein engineering in the deep learning era by Bingxin Zhou, Yang Tan, Yutong Hu, Lirong Zheng, Bozitao Zhong, Liang Hong

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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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S‐PLM: Structure‐Aware Protein Language Model via Contrastive Learning Between Sequence and Structure by Duolin Wang, Mahdi Pourmirzaei, Usman L. Abbas, Shuai Zeng, Negin Manshour, Farzaneh Esmaili, Biplab Poudel, Yuexu Jiang, Qing Shao, Jin Chen, Dong Xu

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PEZy-miner: An artificial intelligence driven approach for the discovery of plastic-degrading enzyme candidates by Renjing Jiang, Zhenrui Yue, Lanyu Shang, Dong Wang, Na Wei

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ProT‐Diff: A Modularized and Efficient Strategy for De Novo Generation of Antimicrobial Peptide Sequences by Integrating Protein Language and Diffusion Models by Xue‐Fei Wang, Jing‐Ya Tang, Jing Sun, Sonam Dorje, Tian‐Qi Sun, Bo Peng, Xu‐Wo Ji, Zhe Li, Xian‐En Zhang, Dian‐Bing Wang

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Parameterized hypercomplex convolutional network for accurate protein backbone torsion angle prediction by Wei Yang, Shujia Wei, Lei 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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DeepBP: Ensemble deep learning strategy for bioactive peptide prediction by Ming Zhang, Jianren Zhou, Xiaohua Wang, Xun Wang, Fang Ge

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Evaluating the advancements in protein language models for encoding strategies in protein function prediction: a comprehensive review by Jia-Ying Chen, Jia-Ying Chen, Jia-Ying Chen, Jing-Fu Wang, Jing-Fu Wang, Jing-Fu Wang, Yue Hu, Yue Hu, Yue Hu, Xin-Hui Li, Xin-Hui Li, Xin-Hui Li, Yu-Rong Qian, Yu-Rong Qian, Yu-Rong Qian, Chao-Lin Song, Chao-Lin Song, Chao-Lin Song

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Protein-small molecule binding site prediction based on a pre-trained protein language model with contrastive learning by Jue Wang, Yufan Liu, Boxue Tian

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