Publications
2026
Xiaogen Zhou, Xiangyu Xu, Guijun Zhang.
When cryo-EM modeling meets structure prediction. Nature Structural & Molecular Biology, 33, 200–202 (2026).
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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.
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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.
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2025
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.
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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.
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Xinyue Cui, Lingyu Ge, Xia Chen, Zexin Lv, Suhui Wang, Xiaogen Zhou, Guijun Zhang.
Beyond static structures: Protein dynamic conformation modeling in the Post-AlphaFold era. Briefings in Bioinformatics, 26(4): bbaf340, 2025.
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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.
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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.
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Wei Zheng, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yang Zhang.
Deep-learning-based single-domain and multidomain protein structure prediction with D-I-TASSER. Nature Biotechnology, 1-13, 2025.
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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, 2025: 115929.
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2015-2024
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.
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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.
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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.
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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.
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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.
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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.
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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, 2022.
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.
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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.
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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.
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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.
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.
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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.
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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.
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.
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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.
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.
Jun Hu, Xiaogen Zhou, Yihen 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.
王柳静, 张贵军, 周晓根.
基于状态估计反馈的策略自适应差分进化算法. 自动化学报, 46(4): 752-766, 2020.
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.
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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, 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.
Xiaogen Zhou, Guijun Zhang, Xiaohu Hao, Li Yu..
A novel differential evolution algorithm using abstract convex underestimate strategy for global optimization. Computers & Operations Research, 75(11): 132-149, 2016.
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.
张贵军, 王柳静, 周晓根, 丁情.
基于共轭增强策略的差分进化算法. 控制与决策, 32(07): 1313-1318, 2017.
周晓根, 张贵军, 郝小虎, 俞立.
一种基于局部Lipschitz下界估计支撑面的差分进化算法. 计算机学报, 39(12): 2631-2651, 2016.
张贵军, 陈铭, 周晓根.
动态小生境半径两阶段多模态差分进化算法. 控制与决策, 31(07): 1185-1191, 2016.
张贵军, 郝小虎, 周晓根, 秦传庆.
动态步长蛋白质构象空间搜索方法. 吉林大学学报, 46(2): 585-594, 2016.
周晓根, 张贵军, 郝小虎.
局部抽象凸区域剖分差分进化算法. 自动化学报, 41(7): 1315-1327, 2015.