Author

Fengyuan Dai

Westlake University

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 3 Bioengineering· 1

Signature Assays, Organisms & Methods

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Assay:protein sequence· 4 Approach:deep learning· 2 Research Focus:protein design· 2 Approach:contrastive learning· 1 Approach:large language model· 1 Approach:machine learning (classical)· 1 Research Focus:protein structure prediction· 1 Research Focus:sequence-to-function modeling· 1

Frequent Co-Authors

Fajie YuaniD· 4 shared Jin SuiD· 4 shared Xibin ZhouiD· 3 shared An‐Ping ZengiD· 2 shared Anthony GitteriD· 2 shared Chenchen HaniD· 2 shared Feng JuiD· 2 shared Qingsong Tan· 2 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 43 mutual co-author links

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4 shared papersBioinformatics

Fajie YuanORCID

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Author profile →

4 papers

Recent·Most cited

Toward De Novo Protein Design from Natural Language

Fengyuan Dai, Shiyang You, Yudian Zhu, Yuan Gao, Lihao Fu, Xibin Zhou, Jin Su, Chentong Wang, Yuliang Fan, Qingsong Tan, Xiaoxiao Ma, Xianjun Deng, Letong Yu, Hui Qian, Yan He, , Fajie Yuan

This paper introduces Pinal, a foundation model that designs proteins from natural language descriptions, achieving functional alignment and experimental success in four design tasks.

Nature · Oct 21, 2026Peer-reviewedBioengineering

DOMINO: Learning Domain Co-occurrence for Multidomain Protein Design

Fengyuan Dai, Jin Su, Qingsong Tan, Huijiao Yang, Xibin Zhou, Fajie Yuan

DOMINO generates multidomain proteins by learning domain co-occurrence patterns and using them to design novel sequences with high structural confidence.

bioRxiv · May 5, 2026 · PreprintBioinformatics

Democratizing Protein Language Model Training, Sharing and Collaboration

Jin Su, Zhikai Li, Tianli Tao, Chenchen Han, Yan He, Fengyuan Dai, Qingyan Yuan, Yuan Gao, Tong Si, Xuting Zhang, Yuyang Zhou, Junjie Shan, Xibin Zhou, Xing Chang, Shiyu Jiang, , Sergey Ovchinnikov

The paper introduces SaprotHub, a platform that simplifies training and sharing of protein language models, enabling non-experts to build and collaborate on customized models.

Nature Biotechnology · Oct 24, 2025Peer-reviewedBioinformatics

Decoding the Molecular Language of Proteins with Evolla

Xibin Zhou, Chenchen Han, Yingqi Zhang, Huan Du, Jiayuan Tian, Jin Su, Renju Liu, Kai Zhuang, Shiyu Jiang, Anthony Gitter, Li Liu, Huayu Li, Meiqi Wu, Shiyang You, Zichen Yuan, , Fajie Yuan

Evolla, a protein-language model, improves functional inference and discovers novel proteins through natural language queries and benchmarking.

bioRxiv · Jan 5, 2025 · PreprintBioinformatics