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Xiaogen Lab

Publications

2026

Xiaogen Zhou, Xiangyu Xu, Guijun Zhang. When cryo-EM modeling meets structure prediction. Nature Structural & Molecular Biology, 33(2): 200-202, 2026. [PDF]
Wei Zheng, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Chunxiang Peng, Yiheng Zhu, Lydia Freddolino, Yang Zhang. Deep-learning-based single-domain and multidomain protein structure prediction with D-I-TASSER. Nature Biotechnology, 44: 641-653, 2026. [PDF] [Hot Paper] [Highly Cited Paper]
Jie Lin, Ziying Zhang, Yu Zhang, Feng Cheng, Chengyuan Wang, Guijun Zhang, Xiaogen Zhou. Enhancing interpretability of cryo-EM maps using hybrid attention Transformers. Cell Reports Physical Science, 7(10): 103596, 2026. [PDF][Server]
Dongliang Hou, Qihang Zhen, Zexin Lv, Xinyue Cui, Suhui Wang, Minghua Hou, Zhan Zhou, Xiaogen Zhou, Guijun Zhang. ProSiteHunter: A unified framework for sequence-based prediction of protein-nucleic acid and protein-protein binding sites. Advanced Science, e75931, 2026. [PDF]
Xinyue Cui, Lingyu Ge, Xinguang Yang, Xuhui Li, Dongliang Hou, Xiaogen Zhou, Guijun Zhang. Exploring protein conformational ensembles using evolutionary conditional diffusion. Journal of Chemical Information and Modeling, in press, 2026. [PDF]
Qiqige Wuyun, Quancheng Liu, Wentao Ni, Chunxiang Peng, Ziying Zhang, Xiaogen Zhou, Gang Hu, Lydia Freddolino, Wei Zheng. Alternative conformation prediction using deep learning with multi-MSA strategy and structural clustering in CASP16. PROTEINS: Structure, Function, and Bioinformatics, 94(1): 348-361, 2026. [PDF]
Chunxiang Peng, Xiaogen Zhou, Jun Liu, Minghua Hou, Stan Z. Li, Guijun Zhang. Multiple conformational states assembly of multidomain proteins using evolutionary algorithm based on structural analogues and sequential homologues. Fundamental Research, 6(1): 77-87, 2026. [PDF]
2025
Ziying Zhang, Liang Xu, Shuai Zhang, Chunxiang Peng, Guijun Zhang, Xiaogen Zhou. DEMO-EMol: Modeling protein-nucleic acid complex structures from cryo-EM maps by coupling chain assembly with map segmentation. Nucleic Acids Research. 53(W1): W228-W237, 2025. [PDF][Server]
Minghua Hou, Yuhao Xia, Pengcheng Wang, Zexin lv, Dongliang Hou, Xiaogen Zhou, Jianyang Zeng, Guijun Zhang. High-accuracy protein complex structure modeling based on sequence-derived structure complementarity. Nature Communications, 16: 10182, 2025. [PDF]
Jing Zou, Wenyi Zhang, Jun Hu, Xiaogen Zhou, Biao Zhang. DockEM: an enhanced method for atomic-scale protein–ligand docking refinement leveraging low-to-medium resolution cryo-EM density maps. Briefings in Bioinformatics, 26(2): bbaf091, 2025. [PDF]
Jun Hu, Yu Zhou, Wenyi Zhang, Xiaogen Zhou. RLEAAI: improving antibody–antigen interaction prediction using protein language model and sequence order information. Briefings in Bioinformatics, 26(3): bbaf238, 2025. [PDF]
Xinyue Cui, Lingyu Ge, Xia Chen, Zexin Lv, Suhui Wang, Xiaogen Zhou, Guijun Zhang. Beyond static structures: protein dynamic conformations modeling in the post-AlphaFold era. Briefings in Bioinformatics, 26(4): bbaf340, 2025. [PDF]
Yaxian Cai, Ziying Zhang, Xiangyu Xu, Liang Xu, Yu Chen, Guijun Zhang, Xiaogen Zhou. Fitting atomic structures into cryo-EM maps by coupling deep learning-enhanced map processing with global-local optimization. Journal of Chemical Information and Modeling, 65(7): 3800-3811, 2025. [PDF][Server]
Jun Liu, Guangxing He, Kailong Zhao, Xiaogen Zhou, Guijun Zhang. De novo protein structure prediction by model quality assessment dynamic feedback mechanism using deep learning. IEEE Transactions on Computational Biology and Bioinformatics, 22(6): 3476-3485, 2025.
Qing Zhang, Youhang Hu, Yu Zhou, Jun Hu, Xiaogen Zhou, Biao Zhang. Improving protein-protein interaction site prediction using graph neural network and structure profiles. Analytical Biochemistry, 705: 115929, 2025. [PDF]
2024
Jing Zhang, Shuo Zhang, Wei Zhou, Xiang Zhang, Guanjin Li, Ruoxuan Li, Xingyu Lin, Ziying Chen, Fang Liu, Pan Shen, Xiaogen Zhou, Yue Gao, Zhenguo Chen, Yanjie Chao, Chengyuan Wang. A widely conserved protein Rof inhibits transcription termination factor Rho and promotes Salmonella virulence program. Nature Communications, 15 (1): 3187, 2024. [PDF]
Ziying Zhang, Yaxian Cai, Biao Zhang, Wei Zheng, Lydia Freddolino, Guijun Zhang, Xiaogen Zhou. DEMO-EM2: Assembling protein complex structures from cryo-EM maps through intertwined chain and domain fitting. Briefings in Bioinformatics, 25(2): bbae113, 2024. [PDF][Server]
2023
Yuhao Xia, Kailong Zhao, Dong Liu, Xiaogen Zhou, Guijun Zhang. Multi-domain and complex protein structure prediction using inter-domain interactions from deep learning. Communications Biology, 6: 1221, 2023.
Kailong Zhao, Yuhao Xia, Fujin Zhang, Xiaogen Zhou, Stan Z. Li, Guijun Zhang. Protein structure and folding pathway prediction based on remote homologs recognition using PAthreader. Communications Biology, 6: 243, 2023.
Zhongze Yu, Chunxiang Peng, Jun Liu, Biao Zhang, Xiaogen Zhou, Guijun Zhang. DomBpred: Protein domain boundary prediction based on domain-residue clustering using inter-residue distance. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 20(2): 912-922, 2023.
2022
Xiaogen Zhou, Wei Zheng, Yang Li, Robin Pearce, Chengxin Zhang, Eric W. Bell, Guijun Zhang, Yang Zhang. I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction. Nature Protocols, 17(10): 2326-2353, 2022. [PDF][Server] [Featured in Nature Protocols] [Hot Paper] [Highly Cited Paper] [2024 Nobel Prize Collection]
Xiaogen Zhou, Yang Li, Chengxin Zhang, Wei Zheng, Guijun Zhang, Yang Zhang. Progressive assembly of multi-domain protein structures from cryo-EM density maps. Nature Computational Science, 2: 265-275, 2022. [PDF][Server]
Xiaogen Zhou, Chunxiang Peng, Wei Zheng, Yang Li, Guijun Zhang, Yang Zhang. DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction. Nucleic Acids Research, 50(W1): W235-W245, 2022. [PDF][Server]
Wei Zheng, Qiqige Wuyun, Xiaogen Zhou, Yang Li, Lydia Freddolino, Yang Zhang. LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation. Nucleic Acids Research, 50(W1): W454–W464, 2022.
Chunxiang Peng, Xiaogen Zhou, Yuhao Xia, Jun Liu, Minghua Hou, Guijun Zhang. Structural analogue-based protein structure domain assembly assisted by deep learning. Bioinformatics, 38(19): 4513-4521, 2022. [PDF]
Saisai Guo, Jun Liu, Xiaogen Zhou, Guijun Zhang. DeepUMQA: Ultrafast shape recognition-based protein model quality assessment using deep learning. Bioinformatics, 38(7): 1895-1903, 2022. [PDF][Server]
Jun Liu, Kailong Zhao, Guangxing He, Liujing Wang, Xiaogen Zhou, Guijun Zhang. A de novo protein structure prediction by iterative partition sampling, topology adjustment and residue-level distance deviation optimization. Bioinformatics, 38(1): 99-107, 2022. [PDF]
Minghua Hou, Chunxiang Peng, Xiaogen Zhou, Biao Zhang, Guijun Zhang. Multi contact-based folding method for de novo protein structure prediction. Briefings in Bioinformatics, 23(1): bbab463, 2022. [PDF]
Chunxiang Peng, Xiaogen Zhou, Guijun Zhang. De novo protein structure prediction by coupling contact with distance profile. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 19(1): 395-406, 2022.
2021
Yuhao Xia, Chunxiang Peng, Xiaogen Zhou, Guijun Zhang. A sequential niche multimodal conformational sampling algorithm for protein structure prediction. Bioinformatics, 37(23): 4357-4365, 2021. [PDF]
Kailong Zhao, Jun Liu, Xiaogen Zhou, Jianzhong Su, Yang Zhang, Guijun Zhang. MMpred: A distance-assisted multimodal conformation sampling for de novo protein structure prediction. Bioinformatics, 37(23): 4350-4356, 2021. [PDF]
Yang Li ,Chengxin Zhang ,Eric W. Bell,Wei Zheng,Xiaogen Zhou,Dong-Jun Yu ,Yang Zhang. Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks. PLoS computational biology, 17(3), e1008865, 2021.
Liujing Wang, Jun Liu, Yuhao Xia, Jiakang Xu, Xiaogen Zhou, Guijun Zhang. Distance-guided protein folding based on generalized descent direction. Briefings in Bioinformatics, 22(6): bbab296, 2021. [PDF]
Wei Zheng, Yang Li, Chengxin Zhang, Xiaogen Zhou, Robin Pearce, Eric W. Bell, Xiaoqiang Huang, Yang Zhang. Protein structure prediction using deep learning distance and hydrogen-bonding restraints in CASP14. Proteins: Structure, Function, and Bioinformatics, 89 (12), 1734-1751, 2021. [Journal Top Cited Article]
Guijun Zhang, Tengyu Xie, Xiaogen Zhou, Liujing Wang, Jun Hu. Protein structure prediction using population-based algorithm guided by information entropy. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 18(2): 697-707, 2021.
Before 2020
Xiaogen Zhou, Chunxiang Peng, Jun Liu, Yang Zhang, Guijun Zhang. Underestimation-assisted global-local cooperative differential evolution and the application to protein structure prediction. IEEE Transactions on Evolutionary Computation, 24(3): 536-550, 2020.
Jun Liu, Xiaogen Zhou, Yang Zhang, Guijun Zhang. CGLFold: A contact-assisted de novo protein structure prediction using global exploration and loop perturbation sampling algorithm. Bioinformatics, 36(8): 2443–2450, 2020. [PDF]
Wei Zheng , Xiaogen Zhou , Qiqige Wuyun , Robin Pearce , Yang Li , Yang Zhang. FUpred: detecting protein domains through deep-learning-based contact map prediction. Bioinformatics, 36(12): 3749–3757, 2020.
Jun Hu, Xiaogen Zhou, Yiheng Zhu, Dongjun Yu, Guijun Zhang. TargetDBP: Accurate DNA-binding protein prediction via sequence-based multi-view feature learning. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 17(4): 1419-1429, 2020.
Guijun Zhang, Laifa Ma, Xiaoqi Wang, Xiaogen Zhou. Secondary structure and contact guided differential evolution for protein structure prediction. IEEE/ACM transactions on computational biology and bioinformatics, 17(3): 1068-1081, 2020.
Guijun Zhang, Xiaoqi Wang, LaiFa Ma, Liujing Wang, Jun Hu, Xiaogen Zhou. Two-stage distance feature-based optimization algorithm for De novo protein structure prediction. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 17(6): 2119-2130, 2020.
Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W. Bell, Xiaogen Zhou, Yang Zhang. Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1. Journal of Proteome Research, 19 (4): 1351-1360., 2020. [Highly Cited Paper]
Xiaogen Zhou, Jun Hu, Chengxin Zhang, Guijun Zhang, Yang Zhang. Assembling multidomain protein structures through analogous global structural alignments. Proceedings of the National Academy of Sciences (PNAS), 116(32): 15930-15938, 2019. [PDF][Server]
Xiaogen Zhou, Guijun Zhang. Differential evolution with underestimation-based multimutation strategy. IEEE Transactions on Cybernetics, 49(4): 1353-1364, 2019.
Zhangwei Li, Ke Sun, Xiaohu Hao, Jun Hu, Laifa Ma, Xiaogen Zhou, Guijun Zhang. Loop enhanced conformational resampling method for protein structure prediction. IEEE Transactions on NanoBioscience, 18(4): 567-577, 2019.
Xiaohu Hao, Guijun Zhang, Xiaogen Zhou. Guiding exploration in conformational feature space with Lipschitz underestimation for ab-initio protein structure prediction. Computational Biology and Chemistry, 73: 105-119, 2018.
Xiaogen Zhou, Guijun Zhang. Abstract convex underestimation assisted multistage differential evolution. IEEE Transactions on Cybernetics, 47(9): 2730-2741, 2017.
Guijun Zhang, Xiaogen Zhou, Xufeng Yu, Xiaohu Hao, Li Yu. Enhancing protein conformational space sampling using distance profile-guided differential evolution. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 14(6): 1288-1301, 2017.
Xiaohu Hao, Guijun Zhang, Xiaogen Zhou. Conformational space sampling method using multi-subpopulation differential evolution for De novo protein structure prediction. IEEE Transactions on NanoBioscience, 16(7): 618-633, 2017.
Xiaogen Zhou, Guijun Zhang, Xiaohu Hao, Li Yu. A novel differential evolution algorithm using local abstract convex underestimate strategy for global optimization. Computers & Operations Research, 75: 132-149, 2016.
Xiaogen Zhou, Guijun Zhang, Xiaohu Hao, Dongwei Xu, Li Yu. Enhanced differential evolution using local Lipschitz underestimate strategy for computationally expensive optimization problems. Applied Soft Computing, 48: 169-181, 2016.
Xiaohu Hao, Guijun Zhang, Xiaogen Zhou, Xufeng Yu. A novel method using abstract convex underestimation in ab-initio protein structure prediction for guiding search in conformational feature space. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 13(5): 887-900, 2016.