Papers with protein engineering
VenusFactory: An Integrated System for Protein Engineering with Data Retrieval and Language Model Fine-Tuning (2025.acl-demo)
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Yang Tan, Chen Liu, Jingyuan Gao, Wu Banghao, Mingchen Li, Ruilin Wang, Lingrong Zhang, Huiqun Yu, Guisheng Fan, Liang Hong, Bingxin Zhou
| Challenge: | Pre-trained protein language models have been used in protein engineering, but their adoption is limited due to data collection, task benchmarking, and application challenges. |
| Approach: | They propose a versatile engine that integrates biological data retrieval, standardized task benchmarking, and modular fine-tuning of PLMs. |
| Outcome: | The proposed engine integrates biological data retrieval, task benchmarking, and modular fine-tuning of PLMs. |
AutoProteinEngine: A Large Language Model Driven Agent Framework for Multimodal AutoML in Protein Engineering (2025.coling-industry)
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| Challenge: | Deep learning models are often inefficient and resource-intensive for biologists without specialized computational expertise. |
| Approach: | They propose an agent framework that leverages large language models for multimodal automated machine learning (AutoML) in protein engineering. |
| Outcome: | The proposed framework demonstrates significant improvements in performance over previous approaches in two real-world protein engineering tasks. |
ProtoCycle: Reflective Tool-Augmented Planning for Text-Guided Protein Design (2026.findings-acl)
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Yutang Ge, Guojiang Zhao, Sihang Li, Zheng Cheng, Zifeng Zhao, Hanchen Xia, Guolin Ke, Linfeng Zhang, Zhifeng Gao, Yu Guang Wang
| Challenge: | Recent deep generative models have already shown encouraging * Equal contribution. |
| Approach: | They propose to use generic instruction-tuned LLMs as direct text-to-sequence generators to achieve this goal. |
| Outcome: | Recent studies show that reflection improves sequence quality and alignment while maintaining competitive foldability. |
Protein Large Language Models: A Comprehensive Survey (2025.findings-emnlp)
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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
| Challenge: | Existing studies focus on specific aspects or applications, but this study provides a comprehensive overview of Protein-specific large language models. |
| Approach: | This paper proposes a structured taxonomy of state-of-the-art ProteinLLMs . they analyze how they leverage large-scale protein sequence data for improved accuracy . |
| Outcome: | The proposed model covers their architectures, training datasets, evaluation metrics, and diverse applications. |