Journal articles on the topic 'Protein language models'
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Tang, Lin. "Protein language models using convolutions." Nature Methods 21, no. 4 (2024): 550. http://dx.doi.org/10.1038/s41592-024-02252-3.
Full textLee, Jin Sub, Osama Abdin, and Philip M. Kim. "Language models for protein design." Current Opinion in Structural Biology 92 (June 2025): 103027. https://doi.org/10.1016/j.sbi.2025.103027.
Full textAli, Sarwan, Prakash Chourasia, and Murray Patterson. "When Protein Structure Embedding Meets Large Language Models." Genes 15, no. 1 (2023): 25. http://dx.doi.org/10.3390/genes15010025.
Full textFerruz, Noelia, and Birte Höcker. "Controllable protein design with language models." Nature Machine Intelligence 4, no. 6 (2022): 521–32. http://dx.doi.org/10.1038/s42256-022-00499-z.
Full textLi, Xiang, Zhuoyu Wei, Yueran Hu, and Xiaolei Zhu. "GraphNABP: Identifying nucleic acid-binding proteins with protein graphs and protein language models." International Journal of Biological Macromolecules 280 (November 2024): 135599. http://dx.doi.org/10.1016/j.ijbiomac.2024.135599.
Full textSingh, Arunima. "Protein language models guide directed antibody evolution." Nature Methods 20, no. 6 (2023): 785. http://dx.doi.org/10.1038/s41592-023-01924-w.
Full textTran, Chau, Siddharth Khadkikar, and Aleksey Porollo. "Survey of Protein Sequence Embedding Models." International Journal of Molecular Sciences 24, no. 4 (2023): 3775. http://dx.doi.org/10.3390/ijms24043775.
Full textPokharel, Suresh, Pawel Pratyush, Hamid D. Ismail, Junfeng Ma, and Dukka B. KC. "Integrating Embeddings from Multiple Protein Language Models to Improve Protein O-GlcNAc Site Prediction." International Journal of Molecular Sciences 24, no. 21 (2023): 16000. http://dx.doi.org/10.3390/ijms242116000.
Full textHu, An, Linai Kuang, and Dinghai Yang. "LPBERT: A Protein–Protein Interaction Prediction Method Based on a Pre-Trained Language Model." Applied Sciences 15, no. 6 (2025): 3283. https://doi.org/10.3390/app15063283.
Full textPang, Yihe, and Bin Liu. "IDP-LM: Prediction of protein intrinsic disorder and disorder functions based on language models." PLOS Computational Biology 19, no. 11 (2023): e1011657. http://dx.doi.org/10.1371/journal.pcbi.1011657.
Full textWeissenow, Konstantin, and Burkhard Rost. "Are protein language models the new universal key?" Current Opinion in Structural Biology 91 (April 2025): 102997. https://doi.org/10.1016/j.sbi.2025.102997.
Full textWang, Wenkai, Zhenling Peng, and Jianyi Yang. "Single-sequence protein structure prediction using supervised transformer protein language models." Nature Computational Science 2, no. 12 (2022): 804–14. http://dx.doi.org/10.1038/s43588-022-00373-3.
Full textZhang, Zitong, Quan Zou, Chunyu Wang, Junjie Wang, and Lingling Zhao. "Improving protein–protein interaction modulator predictions via knowledge-fused language models." Information Fusion 123 (November 2025): 103227. https://doi.org/10.1016/j.inffus.2025.103227.
Full textKenlay, Henry, Frédéric A. Dreyer, Aleksandr Kovaltsuk, Dom Miketa, Douglas Pires, and Charlotte M. Deane. "Large scale paired antibody language models." PLOS Computational Biology 20, no. 12 (2024): e1012646. https://doi.org/10.1371/journal.pcbi.1012646.
Full textZhao, Long, Qiang He, Huijia Song, et al. "Protein A-like Peptide Design Based on Diffusion and ESM2 Models." Molecules 29, no. 20 (2024): 4965. http://dx.doi.org/10.3390/molecules29204965.
Full textQu, Yang, Zitong Niu, Qiaojiao Ding, et al. "Ensemble Learning with Supervised Methods Based on Large-Scale Protein Language Models for Protein Mutation Effects Prediction." International Journal of Molecular Sciences 24, no. 22 (2023): 16496. http://dx.doi.org/10.3390/ijms242216496.
Full textWeber, Leon, Kirsten Thobe, Oscar Arturo Migueles Lozano, Jana Wolf, and Ulf Leser. "PEDL: extracting protein–protein associations using deep language models and distant supervision." Bioinformatics 36, Supplement_1 (2020): i490—i498. http://dx.doi.org/10.1093/bioinformatics/btaa430.
Full textWang, Yang. "Enhanced protein function prediction by fusion embedding based on protein language models." Highlights in Science, Engineering and Technology 66 (September 20, 2023): 177–84. http://dx.doi.org/10.54097/hset.v66i.11697.
Full textSun, Yuanfei, and Yang Shen. "Variant effect prediction using structure-informed protein language models." Biophysical Journal 122, no. 3 (2023): 473a. http://dx.doi.org/10.1016/j.bpj.2022.11.2537.
Full textThumuluri, Vineet, Hannah-Marie Martiny, Jose J. Almagro Armenteros, Jesper Salomon, Henrik Nielsen, and Alexander Rosenberg Johansen. "NetSolP: predicting protein solubility in Escherichia coli using language models." Bioinformatics 38, no. 4 (2021): 941–46. http://dx.doi.org/10.1093/bioinformatics/btab801.
Full textWang, Bo, and Wenjin Li. "Advances in the Application of Protein Language Modeling for Nucleic Acid Protein Binding Site Prediction." Genes 15, no. 8 (2024): 1090. http://dx.doi.org/10.3390/genes15081090.
Full textDeutschmann, Nicolas, Aurelien Pelissier, Anna Weber, Shuaijun Gao, Jasmina Bogojeska, and María Rodríguez Martínez. "Do domain-specific protein language models outperform general models on immunology-related tasks?" ImmunoInformatics 14 (June 2024): 100036. http://dx.doi.org/10.1016/j.immuno.2024.100036.
Full textMardikoraem, Mehrsa, and Daniel Woldring. "Protein Fitness Prediction Is Impacted by the Interplay of Language Models, Ensemble Learning, and Sampling Methods." Pharmaceutics 15, no. 5 (2023): 1337. http://dx.doi.org/10.3390/pharmaceutics15051337.
Full textBhat, Suhaas, Garyk Brixi, Kalyan Palepu, et al. "Abstract C118: Design of programmable peptide-guided oncoprotein degraders via generative language models." Molecular Cancer Therapeutics 22, no. 12_Supplement (2023): C118. http://dx.doi.org/10.1158/1535-7163.targ-23-c118.
Full textLiu, Dan, Francesca Young, Kieran D. Lamb, David L. Robertson, and Ke Yuan. "Prediction of virus-host associations using protein language models and multiple instance learning." PLOS Computational Biology 20, no. 11 (2024): e1012597. http://dx.doi.org/10.1371/journal.pcbi.1012597.
Full textYadalam, Pradeep kumar, Ramya Ramadoss, Pradeep kumar R, and Jishnu Krishna Kumar. "Pre-Trained Language Models Based Sequence Prediction of Wnt-Sclerostin Protein Sequences in Alveolar Bone Formation." Journal of Pioneering Medical Science 12, no. 3 (2023): 55–60. http://dx.doi.org/10.61091/jpms202312311.
Full textNana Teukam, Yves Gaetan, Loïc Kwate Dassi, Matteo Manica, Daniel Probst, Philippe Schwaller, and Teodoro Laino. "Language models can identify enzymatic binding sites in protein sequences." Computational and Structural Biotechnology Journal 23 (December 2024): 1929–37. http://dx.doi.org/10.1016/j.csbj.2024.04.012.
Full textZhu, Yi-Heng, Chengxin Zhang, Dong-Jun Yu, and Yang Zhang. "Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction." PLOS Computational Biology 18, no. 12 (2022): e1010793. http://dx.doi.org/10.1371/journal.pcbi.1010793.
Full textValentini, Giorgio, Dario Malchiodi, Jessica Gliozzo, et al. "The promises of large language models for protein design and modeling." Frontiers in Bioinformatics 3 (November 23, 2023). http://dx.doi.org/10.3389/fbinf.2023.1304099.
Full textMall, Raghvendra, Rahul Kaushik, Zachary A. Martinez, Matt W. Thomson, and Filippo Castiglione. "Benchmarking protein language models for protein crystallization." Scientific Reports 15, no. 1 (2025). https://doi.org/10.1038/s41598-025-86519-5.
Full textUnsal, Serbulent, Heval Ataş, Muammer Albayrak, Kemal Turhan, Aybar C. Acar, and Tunca Doğan. "Learning Functional Properties of Proteins with Language Models." October 28, 2020. https://doi.org/10.5281/zenodo.5795850.
Full textAvraham, Orly, Tomer Tsaban, Ziv Ben-Aharon, Linoy Tsaban, and Ora Schueler-Furman. "Protein language models can capture protein quaternary state." BMC Bioinformatics 24, no. 1 (2023). http://dx.doi.org/10.1186/s12859-023-05549-w.
Full textBoshar, Sam, Evan Trop, Bernardo P. de Almeida, Liviu Copoiu, and Thomas Pierrot. "Are Genomic Language Models All You Need? Exploring Genomic Language Models on Protein Downstream Tasks." Bioinformatics, August 30, 2024. http://dx.doi.org/10.1093/bioinformatics/btae529.
Full textAn, Jingmin, and Xiaogang Weng. "Collectively encoding protein properties enriches protein language models." BMC Bioinformatics 23, no. 1 (2022). http://dx.doi.org/10.1186/s12859-022-05031-z.
Full textNarang, Kush, Abhigyan Nath, William Hemstrom, and Simon K. S. Chu. "HaloClass: Salt-Tolerant Protein Classification with Protein Language Models." Protein Journal, October 21, 2024. http://dx.doi.org/10.1007/s10930-024-10236-7.
Full textTule, Sanjana, Gabriel Foley, and Mikael Bodén. "Do protein language models learn phylogeny?" Briefings in Bioinformatics 26, no. 1 (2024). https://doi.org/10.1093/bib/bbaf047.
Full textVitale, Rosario, Leandro A. Bugnon, Emilio Luis Fenoy, Diego H. Milone, and Georgina Stegmayer. "Evaluating large language models for annotating proteins." Briefings in Bioinformatics 25, no. 3 (2024). http://dx.doi.org/10.1093/bib/bbae177.
Full textMcWhite, Claire Darnell, Isabel Armour-Garb, and Mona Singh. "Leveraging protein language models for accurate multiple sequence alignments." Genome Research, July 6, 2023, gr.277675.123. http://dx.doi.org/10.1101/gr.277675.123.
Full textJing, Xiaoyang, Fandi Wu, Xiao Luo, and Jinbo Xu. "Single-sequence protein structure prediction by integrating protein language models." Proceedings of the National Academy of Sciences 121, no. 13 (2024). http://dx.doi.org/10.1073/pnas.2308788121.
Full textPeicong, Lin, Tao Huanyu, Li Hao, and Huang Sheng-You. "Protein-protein contact prediction by geometric triangle-aware protein language models." August 31, 2023. https://doi.org/10.5281/zenodo.8304327.
Full textHaselbeck, Florian, Maura John, Yuqi Zhang, et al. "Superior protein thermophilicity prediction with protein language model embeddings." NAR Genomics and Bioinformatics 5, no. 4 (2023). http://dx.doi.org/10.1093/nargab/lqad087.
Full textLin, Peicong, Huanyu Tao, Hao Li, and Sheng-You Huang. "Protein–protein contact prediction by geometric triangle-aware protein language models." Nature Machine Intelligence, October 19, 2023. http://dx.doi.org/10.1038/s42256-023-00741-2.
Full textIeremie, Ioan, Rob M. Ewing, and Mahesan Niranjan. "Protein language models meet reduced amino acid alphabets." Bioinformatics, February 3, 2024. http://dx.doi.org/10.1093/bioinformatics/btae061.
Full textKabir, Anowarul, Asher Moldwin, Yana Bromberg, and Amarda Shehu. "In the Twilight Zone of Protein Sequence Homology: Do Protein Language Models Learn Protein Structure?" Bioinformatics Advances, August 17, 2024. http://dx.doi.org/10.1093/bioadv/vbae119.
Full textPudžiuvelytė, Ieva, Kliment Olechnovič, Egle Godliauskaite, et al. "TemStaPro: protein thermostability prediction using sequence representations from protein language models." Bioinformatics, March 20, 2024. http://dx.doi.org/10.1093/bioinformatics/btae157.
Full textChen, Bo, Ziwei Xie, Jiezhong Qiu, Zhaofeng Ye, Jinbo Xu, and Jie Tang. "Improved the heterodimer protein complex prediction with protein language models." Briefings in Bioinformatics, June 16, 2023. http://dx.doi.org/10.1093/bib/bbad221.
Full textXiang, Wenkai, Zhaoping Xiong, Huan Chen, et al. "FAPM: Functional Annotation of Proteins using Multi-Modal Models Beyond Structural Modeling." Bioinformatics, November 14, 2024. http://dx.doi.org/10.1093/bioinformatics/btae680.
Full textTang Tian-Yi, Xiong Yi-Ming, Zhang Rui-Ge, et al. "Progress in Protein Pre-training Models Integrated with Structural Knowledge." Acta Physica Sinica, 2024, 0. http://dx.doi.org/10.7498/aps.73.20240811.
Full textSun, Yuanfei, and Yang Shen. "Structure-Informed Protein Language Models are Robust Predictors for Variants Effects." July 30, 2023. https://doi.org/10.5281/zenodo.8197882.
Full textMarquet, Céline, Michael Heinzinger, Tobias Olenyi, et al. "Embeddings from protein language models predict conservation and variant effects." Human Genetics, December 30, 2021. http://dx.doi.org/10.1007/s00439-021-02411-y.
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