Author

You Xu

Shihezi 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· 2 Bioengineering· 1 Biophysics· 1

Signature Assays, Organisms & Methods

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Research Focus:drug response / drug discovery· 2 Approach:machine learning (classical)· 2 Research Focus:benchmarking· 1 Approach:experimental assay· 1 Approach:graph neural network· 1 Organism:mouse· 1 Assay:proteomics· 1 Approach:statistical model· 1

Frequent Co-Authors

Shengwen YangiD· 2 shared Zhenming LiuiD· 2 shared Zhuoyan Liu· 2 shared Bin DaiiD· 1 shared Bo WeniD· 1 shared Chunpeng Yang· 1 shared Duxin SuniD· 1 shared Furong ChengiD· 1 shared

Activity by Year

2024-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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2 shared papersBioinformatics

Shengwen YangORCID

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Author profile →

4 papers

Recent·Most cited

Tractable and Thermodynamically Consistent pKa Prediction via First-Dissociation Aggregation

Zhuoyan Liu, Qiuyin Zhu, Qingkun Li, Yuanxi Zhu, You Xu, Bin Dai, Yongsheng Li, Zhenming Liu, Shengwen Yang

This paper introduces DTi-pKa, a graph neural network that predicts pKa values with thermodynamic consistency and achieves high accuracy on benchmark datasets.

bioRxiv · Oct 6, 2026 · PreprintBioinformatics

Pair-complete structural gating enables Pareto optimization of de novo cyclic peptides with preserved binding geometry and improved developability

Yuanchao Hou, Yixin Zhang, Zhuoyan Liu, 彭新发, Ziye Liu, Miyesier Yusupujiang, You Xu, Jiaxin Hu, Zhenming Liu, Shengwen Yang

This paper introduces RF-PepTune, a method that improves cyclic peptide design by preserving binding geometry while optimizing multiple properties, achieving higher success rates in structural and functional criteria.

bioRxiv · Sep 29, 2026 · PreprintBioinformatics

Benchmarking Universal Machine Learning Force Fields with Hydrogen-Bonding Cooperativity

Xinping Feng, You Xu, Jing Huang

This study benchmarks three MLFF models on their ability to capture hydrogen-bond cooperativity in N-methylacetamide polymers, finding MACE-OFF most accurate.

Communications in Computational Chemistry · Jun 9, 2025Peer-reviewedBiophysics

Proteolysis-targeting vaccines (PROTAVs) for robust combination immunotherapy of melanoma

Qiyan Wang, Ting Su, Furong Cheng, Shurong Zhou, Xiang Liu, Mi Wang, You Xu, Ri Tang, Shimiao Liao, Jordan M. Dailey, Guolan Xiao, Chunpeng Yang, Hanning Wen, Weijia Zheng, Bo Wen, , Guizhi Zhu

This paper introduces PROTAVs, a new vaccine strategy that enhances T cell responses and combination immunotherapy for melanoma by improving antigen processing and cross-presentation.

bioRxiv · Oct 1, 2024 · PreprintBioengineering