Artículos de revistas sobre el tema "Protein language models"
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Tang, Lin. "Protein language models using convolutions". Nature Methods 21, n.º 4 (abril de 2024): 550. http://dx.doi.org/10.1038/s41592-024-02252-3.
Texto completoAli, Sarwan, Prakash Chourasia y Murray Patterson. "When Protein Structure Embedding Meets Large Language Models". Genes 15, n.º 1 (23 de diciembre de 2023): 25. http://dx.doi.org/10.3390/genes15010025.
Texto completoFerruz, Noelia y Birte Höcker. "Controllable protein design with language models". Nature Machine Intelligence 4, n.º 6 (junio de 2022): 521–32. http://dx.doi.org/10.1038/s42256-022-00499-z.
Texto completoLi, Xiang, Zhuoyu Wei, Yueran Hu y Xiaolei Zhu. "GraphNABP: Identifying nucleic acid-binding proteins with protein graphs and protein language models". International Journal of Biological Macromolecules 280 (noviembre de 2024): 135599. http://dx.doi.org/10.1016/j.ijbiomac.2024.135599.
Texto completoSingh, Arunima. "Protein language models guide directed antibody evolution". Nature Methods 20, n.º 6 (junio de 2023): 785. http://dx.doi.org/10.1038/s41592-023-01924-w.
Texto completoTran, Chau, Siddharth Khadkikar y Aleksey Porollo. "Survey of Protein Sequence Embedding Models". International Journal of Molecular Sciences 24, n.º 4 (14 de febrero de 2023): 3775. http://dx.doi.org/10.3390/ijms24043775.
Texto completoPokharel, Suresh, Pawel Pratyush, Hamid D. Ismail, Junfeng Ma y Dukka B. KC. "Integrating Embeddings from Multiple Protein Language Models to Improve Protein O-GlcNAc Site Prediction". International Journal of Molecular Sciences 24, n.º 21 (6 de noviembre de 2023): 16000. http://dx.doi.org/10.3390/ijms242116000.
Texto completoWang, Wenkai, Zhenling Peng y Jianyi Yang. "Single-sequence protein structure prediction using supervised transformer protein language models". Nature Computational Science 2, n.º 12 (19 de diciembre de 2022): 804–14. http://dx.doi.org/10.1038/s43588-022-00373-3.
Texto completoPang, Yihe y Bin Liu. "IDP-LM: Prediction of protein intrinsic disorder and disorder functions based on language models". PLOS Computational Biology 19, n.º 11 (22 de noviembre de 2023): e1011657. http://dx.doi.org/10.1371/journal.pcbi.1011657.
Texto completoWeber, Leon, Kirsten Thobe, Oscar Arturo Migueles Lozano, Jana Wolf y Ulf Leser. "PEDL: extracting protein–protein associations using deep language models and distant supervision". Bioinformatics 36, Supplement_1 (1 de julio de 2020): i490—i498. http://dx.doi.org/10.1093/bioinformatics/btaa430.
Texto completoWang, Yang. "Enhanced protein function prediction by fusion embedding based on protein language models". Highlights in Science, Engineering and Technology 66 (20 de septiembre de 2023): 177–84. http://dx.doi.org/10.54097/hset.v66i.11697.
Texto completoSun, Yuanfei y Yang Shen. "Variant effect prediction using structure-informed protein language models". Biophysical Journal 122, n.º 3 (febrero de 2023): 473a. http://dx.doi.org/10.1016/j.bpj.2022.11.2537.
Texto completoQu, Yang, Zitong Niu, Qiaojiao Ding, Taowa Zhao, Tong Kong, Bing Bai, Jianwei Ma, Yitian Zhao y Jianping Zheng. "Ensemble Learning with Supervised Methods Based on Large-Scale Protein Language Models for Protein Mutation Effects Prediction". International Journal of Molecular Sciences 24, n.º 22 (18 de noviembre de 2023): 16496. http://dx.doi.org/10.3390/ijms242216496.
Texto completoThumuluri, Vineet, Hannah-Marie Martiny, Jose J. Almagro Armenteros, Jesper Salomon, Henrik Nielsen y Alexander Rosenberg Johansen. "NetSolP: predicting protein solubility in Escherichia coli using language models". Bioinformatics 38, n.º 4 (27 de noviembre de 2021): 941–46. http://dx.doi.org/10.1093/bioinformatics/btab801.
Texto completoDeutschmann, Nicolas, Aurelien Pelissier, Anna Weber, Shuaijun Gao, Jasmina Bogojeska y María Rodríguez Martínez. "Do domain-specific protein language models outperform general models on immunology-related tasks?" ImmunoInformatics 14 (junio de 2024): 100036. http://dx.doi.org/10.1016/j.immuno.2024.100036.
Texto completoWang, Bo y Wenjin Li. "Advances in the Application of Protein Language Modeling for Nucleic Acid Protein Binding Site Prediction". Genes 15, n.º 8 (18 de agosto de 2024): 1090. http://dx.doi.org/10.3390/genes15081090.
Texto completoBhat, Suhaas, Garyk Brixi, Kalyan Palepu, Lauren Hong, Vivian Yudistyra, Tianlai Chen, Sophia Vincoff, Lin Zhao y Pranam Chatterjee. "Abstract C118: Design of programmable peptide-guided oncoprotein degraders via generative language models". Molecular Cancer Therapeutics 22, n.º 12_Supplement (1 de diciembre de 2023): C118. http://dx.doi.org/10.1158/1535-7163.targ-23-c118.
Texto completoMardikoraem, Mehrsa y Daniel Woldring. "Protein Fitness Prediction Is Impacted by the Interplay of Language Models, Ensemble Learning, and Sampling Methods". Pharmaceutics 15, n.º 5 (25 de abril de 2023): 1337. http://dx.doi.org/10.3390/pharmaceutics15051337.
Texto completoNana Teukam, Yves Gaetan, Loïc Kwate Dassi, Matteo Manica, Daniel Probst, Philippe Schwaller y Teodoro Laino. "Language models can identify enzymatic binding sites in protein sequences". Computational and Structural Biotechnology Journal 23 (diciembre de 2024): 1929–37. http://dx.doi.org/10.1016/j.csbj.2024.04.012.
Texto completoYadalam, Pradeep kumar, Ramya Ramadoss, Pradeep kumar R y 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, n.º 3 (31 de diciembre de 2023): 55–60. http://dx.doi.org/10.61091/jpms202312311.
Texto completoWang, Yan, Huiting Sun, Nan Sheng, Kai He, Wenjv Hou, Ziqi Zhao, Qixing Yang y Lan Huang. "ESMSec: Prediction of Secreted Proteins in Human Body Fluids Using Protein Language Models and Attention". International Journal of Molecular Sciences 25, n.º 12 (9 de junio de 2024): 6371. http://dx.doi.org/10.3390/ijms25126371.
Texto completoZhu, Yi-Heng, Chengxin Zhang, Dong-Jun Yu y Yang Zhang. "Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction". PLOS Computational Biology 18, n.º 12 (22 de diciembre de 2022): e1010793. http://dx.doi.org/10.1371/journal.pcbi.1010793.
Texto completoLin, Zeming, Halil Akin, Roshan Rao, Brian Hie, Zhongkai Zhu, Wenting Lu, Nikita Smetanin et al. "Evolutionary-scale prediction of atomic-level protein structure with a language model". Science 379, n.º 6637 (17 de marzo de 2023): 1123–30. http://dx.doi.org/10.1126/science.ade2574.
Texto completoStrodthoff, Nils, Patrick Wagner, Markus Wenzel y Wojciech Samek. "UDSMProt: universal deep sequence models for protein classification". Bioinformatics 36, n.º 8 (8 de enero de 2020): 2401–9. http://dx.doi.org/10.1093/bioinformatics/btaa003.
Texto completoGonzales, Mark Edward M., Jennifer C. Ureta y Anish M. S. Shrestha. "Protein embeddings improve phage-host interaction prediction". PLOS ONE 18, n.º 7 (24 de julio de 2023): e0289030. http://dx.doi.org/10.1371/journal.pone.0289030.
Texto completoBecker, Felix y Mario Stanke. "learnMSA2: deep protein multiple alignments with large language and hidden Markov models". Bioinformatics 40, Supplement_2 (1 de septiembre de 2024): ii79—ii86. http://dx.doi.org/10.1093/bioinformatics/btae381.
Texto completoOuteiral, Carlos y Charlotte M. Deane. "Codon language embeddings provide strong signals for use in protein engineering". Nature Machine Intelligence 6, n.º 2 (23 de febrero de 2024): 170–79. http://dx.doi.org/10.1038/s42256-024-00791-0.
Texto completoMedina-Ortiz, David, Seba Contreras, Diego Fernández, Nicole Soto-García, Iván Moya, Gabriel Cabas-Mora y Álvaro Olivera-Nappa. "Protein Language Models and Machine Learning Facilitate the Identification of Antimicrobial Peptides". International Journal of Molecular Sciences 25, n.º 16 (14 de agosto de 2024): 8851. http://dx.doi.org/10.3390/ijms25168851.
Texto completoChu, Hongkang y Taigang Liu. "Comprehensive Research on Druggable Proteins: From PSSM to Pre-Trained Language Models". International Journal of Molecular Sciences 25, n.º 8 (19 de abril de 2024): 4507. http://dx.doi.org/10.3390/ijms25084507.
Texto completoPang, Yihe y Bin Liu. "DMFpred: Predicting protein disorder molecular functions based on protein cubic language model". PLOS Computational Biology 18, n.º 10 (31 de octubre de 2022): e1010668. http://dx.doi.org/10.1371/journal.pcbi.1010668.
Texto completoValentini, Giorgio, Dario Malchiodi, Jessica Gliozzo, Marco Mesiti, Mauricio Soto-Gomez, Alberto Cabri, Justin Reese, Elena Casiraghi y Peter N. Robinson. "The promises of large language models for protein design and modeling". Frontiers in Bioinformatics 3 (23 de noviembre de 2023). http://dx.doi.org/10.3389/fbinf.2023.1304099.
Texto completoAvraham, Orly, Tomer Tsaban, Ziv Ben-Aharon, Linoy Tsaban y Ora Schueler-Furman. "Protein language models can capture protein quaternary state". BMC Bioinformatics 24, n.º 1 (14 de noviembre de 2023). http://dx.doi.org/10.1186/s12859-023-05549-w.
Texto completoBoshar, Sam, Evan Trop, Bernardo P. de Almeida, Liviu Copoiu y Thomas Pierrot. "Are Genomic Language Models All You Need? Exploring Genomic Language Models on Protein Downstream Tasks". Bioinformatics, 30 de agosto de 2024. http://dx.doi.org/10.1093/bioinformatics/btae529.
Texto completoAn, Jingmin y Xiaogang Weng. "Collectively encoding protein properties enriches protein language models". BMC Bioinformatics 23, n.º 1 (8 de noviembre de 2022). http://dx.doi.org/10.1186/s12859-022-05031-z.
Texto completoMcWhite, Claire Darnell, Isabel Armour-Garb y Mona Singh. "Leveraging protein language models for accurate multiple sequence alignments". Genome Research, 6 de julio de 2023, gr.277675.123. http://dx.doi.org/10.1101/gr.277675.123.
Texto completoJing, Xiaoyang, Fandi Wu, Xiao Luo y Jinbo Xu. "Single-sequence protein structure prediction by integrating protein language models". Proceedings of the National Academy of Sciences 121, n.º 13 (20 de marzo de 2024). http://dx.doi.org/10.1073/pnas.2308788121.
Texto completoVitale, Rosario, Leandro A. Bugnon, Emilio Luis Fenoy, Diego H. Milone y Georgina Stegmayer. "Evaluating large language models for annotating proteins". Briefings in Bioinformatics 25, n.º 3 (27 de marzo de 2024). http://dx.doi.org/10.1093/bib/bbae177.
Texto completoLin, Peicong, Huanyu Tao, Hao Li y Sheng-You Huang. "Protein–protein contact prediction by geometric triangle-aware protein language models". Nature Machine Intelligence, 19 de octubre de 2023. http://dx.doi.org/10.1038/s42256-023-00741-2.
Texto completoHaselbeck, Florian, Maura John, Yuqi Zhang, Jonathan Pirnay, Juan Pablo Fuenzalida-Werner, Rubén D. Costa y Dominik G. Grimm. "Superior protein thermophilicity prediction with protein language model embeddings". NAR Genomics and Bioinformatics 5, n.º 4 (11 de octubre de 2023). http://dx.doi.org/10.1093/nargab/lqad087.
Texto completoIeremie, Ioan, Rob M. Ewing y Mahesan Niranjan. "Protein language models meet reduced amino acid alphabets". Bioinformatics, 3 de febrero de 2024. http://dx.doi.org/10.1093/bioinformatics/btae061.
Texto completoPudžiuvelytė, Ieva, Kliment Olechnovič, Egle Godliauskaite, Kristupas Sermokas, Tomas Urbaitis, Giedrius Gasiunas y Darius Kazlauskas. "TemStaPro: protein thermostability prediction using sequence representations from protein language models". Bioinformatics, 20 de marzo de 2024. http://dx.doi.org/10.1093/bioinformatics/btae157.
Texto completoKabir, Anowarul, Asher Moldwin, Yana Bromberg y Amarda Shehu. "In the Twilight Zone of Protein Sequence Homology: Do Protein Language Models Learn Protein Structure?" Bioinformatics Advances, 17 de agosto de 2024. http://dx.doi.org/10.1093/bioadv/vbae119.
Texto completoChen, Bo, Ziwei Xie, Jiezhong Qiu, Zhaofeng Ye, Jinbo Xu y Jie Tang. "Improved the heterodimer protein complex prediction with protein language models". Briefings in Bioinformatics, 16 de junio de 2023. http://dx.doi.org/10.1093/bib/bbad221.
Texto completoTang Tian-Yi, Xiong Yi-Ming, Zhang Rui-Ge, Zhang Jian, Li Wen-Fei, Wang Jun y Wang Wei. "Progress in Protein Pre-training Models Integrated with Structural Knowledge". Acta Physica Sinica, 2024, 0. http://dx.doi.org/10.7498/aps.73.20240811.
Texto completoLivesey, Benjamin J. y Joseph A. Marsh. "Advancing variant effect prediction using protein language models". Nature Genetics, 10 de agosto de 2023. http://dx.doi.org/10.1038/s41588-023-01470-3.
Texto completoNijkamp, Erik, Jeffrey A. Ruffolo, Eli N. Weinstein, Nikhil Naik y Ali Madani. "ProGen2: Exploring the boundaries of protein language models". Cell Systems, octubre de 2023. http://dx.doi.org/10.1016/j.cels.2023.10.002.
Texto completoMarquet, Céline, Michael Heinzinger, Tobias Olenyi, Christian Dallago, Kyra Erckert, Michael Bernhofer, Dmitrii Nechaev y Burkhard Rost. "Embeddings from protein language models predict conservation and variant effects". Human Genetics, 30 de diciembre de 2021. http://dx.doi.org/10.1007/s00439-021-02411-y.
Texto completoSi, Yunda y Chengfei Yan. "Improved inter-protein contact prediction using dimensional hybrid residual networks and protein language models". Briefings in Bioinformatics, 9 de febrero de 2023. http://dx.doi.org/10.1093/bib/bbad039.
Texto completoHarrigan, William L., Barbra D. Ferrell, K. Eric Wommack, Shawn W. Polson, Zachary D. Schreiber y Mahdi Belcaid. "Improvements in viral gene annotation using large language models and soft alignments". BMC Bioinformatics 25, n.º 1 (25 de abril de 2024). http://dx.doi.org/10.1186/s12859-024-05779-6.
Texto completoHie, Brian L., Kevin K. Yang y Peter S. Kim. "Evolutionary velocity with protein language models predicts evolutionary dynamics of diverse proteins". Cell Systems, febrero de 2022. http://dx.doi.org/10.1016/j.cels.2022.01.003.
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