Protein Large Language Models: A Comprehensive Survey

• URL: http://arxiv.org/abs/2502.17504v2
• Date: Thu, 06 Mar 2025 16:14:45 GMT
• Title: Protein Large Language Models: A Comprehensive Survey
• Authors: Yijia Xiao, Wanjia Zhao, Junkai Zhang, Yiqiao Jin, Han Zhang, Zhicheng Ren, Renliang Sun, Haixin Wang, Guancheng Wan, Pan Lu, Xiao Luo, Yu Zhang, James Zou, Yizhou Sun, Wei Wang,
• Abstract summary: Protein-specific large language models (Protein LLMs) are revolutionizing protein science by enabling more efficient protein structure prediction, function annotation, and design.<n>This work provides the first comprehensive overview of Protein LLMs, covering their architectures, training datasets, evaluation metrics, and diverse applications.
• Score: 71.65899614084853
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: Protein-specific large language models (Protein LLMs) are revolutionizing protein science by enabling more efficient protein structure prediction, function annotation, and design. While existing surveys focus on specific aspects or applications, this work provides the first comprehensive overview of Protein LLMs, covering their architectures, training datasets, evaluation metrics, and diverse applications. Through a systematic analysis of over 100 articles, we propose a structured taxonomy of state-of-the-art Protein LLMs, analyze how they leverage large-scale protein sequence data for improved accuracy, and explore their potential in advancing protein engineering and biomedical research. Additionally, we discuss key challenges and future directions, positioning Protein LLMs as essential tools for scientific discovery in protein science. Resources are maintained at https://github.com/Yijia-Xiao/Protein-LLM-Survey.

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