发表论文 Journal Articles
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, in press, 2025.

  • Dong Liu, Jun Liu, Haodong Wang, Fang Liang, Guijun Zhang.
    DeepUMQA-X Web Server: Comprehensive and Insightful Estimation of Model Accuracy for Protein Single-chain and Complex.
    Nucleic Acids Research, in press, 2025.

  • Xinyue Cui, Yuhao Xia, Minghua Hou, Xuanfeng Zhao, Suhui Wang, Guijun Zhang.
    M-DeepAssembly: enhanced DeepAssembly based on multi-objective multi-domain protein conformation sampling.
    BMC Bioinformatics, in press, 2025.

  • Yuhao Xia, Yilin Pu, Suhui Wang, Jianan Zhuang, Dong Liu, Minghua Hou, Guijun Zhang.
    DeepAssembly2: A Web Server for Protein Complex Structure Assembly Based on Domain-Domain Interactions.
    Journal of Molecular Biology, in press, 2025.

  • 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, in press, 2025.

  • Haodong Wang, Meng Sun, Lei Xie, Dong Liu, Guijun Zhang.
    Physical-aware model accuracy estimation for protein complex using deep learning method.
    Computational and Structural Biotechnology Journal, 27: 478-487, 2025.

  • 蒲奕霖，王苏慧，夏瑜豪，张贵军.
    蛋白质复合物链间残基距离深度学习预测方法.
    中国科学: 信息科学, 55(1): 94-109, 2025.

2024

  • Fujin Zhang, Zhangwei Li, Kailong Zhao, Pengxin Zhao, Guijun Zhang.
    Prediction of Inter-residue Multiple Distances and Exploration of Protein Multiple Conformations by Deep Learning.
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, PP: 1-9, 2024.

  • Kailong Zhao, Pengxin Zhao, Suhui Wang, Yuhao Xia, Guijun Zhang.
    FoldPAthreader: predicting protein folding pathway using a novel folding force field model derived from known protein universe.
    Genome Biology, 25: 152, 2024.

  • 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, in press, 2024.

  • Fang Liang, Meng Sun, Lei Xie, Xuanfeng Zhao, Dong Liu, Kailong Zhao, Guijun Zhang.
    Recent advances and challenges in protein complex model accuracy estimation.
    Computational and Structural Biotechnology Journal, 23: 1824-1832, 2024.

  • Hui Wang, Dong Liu, Kailong Zhao, Yajun Wang, Guijun Zhang.
    SPDesign: protein sequence designer based on structural sequence profile using ultrafast shape recognition.
    Briefings in Bioinformatics, 25(3): bbae146, 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.

  • Dong Liu, Biao Zhang, Jun Liu, Hui Li, Le Song, Guijun Zhang.
    Assessing protein model quality based on deep graph coupled networks using protein language model.
    Briefings in Bioinformatics, 25(1): bbad420, 2024.

2023

  • Chunxiang Peng, Fang Liang, Yuhao Xia, Kailong Zhao, Minghua Hou, Guijun Zhang.
    Recent advances and challenges in protein structure prediction.
    Journal of Chemical Information and Modeling, 64(1): 76-95, 2023.

  • Minghua Hou, Sirong Jin, Xinyue Cui, Chunxiang Peng, Kailong Zhao, Le Song, Guijun Zhang.
    Protein Multiple Conformations Prediction Using Multi-Objective Evolution Algorithm.
    Interdisciplinary Sciences:Computational Life Sciences, (2024): 1-13, 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.

  • Jun Liu, Dong Liu, Guijun Zhang.
    DeepUMQA3: a web server for accurate assessment of interface residue accuracy in protein complexes.
    Bioinformatics, 39(10): btad591, 2023.

  • Haitao Zhu, Yuhao Xia, Guijun Zhang.
    E2EDA: Protein domain assembly based on end-to-end deep learning.
    Journal of Chemical Information and Modeling, 63(20): 6451-6461, 2023.

  • 刘栋，崔新月，王浩东，张贵军.
    蛋白质结构模型质量评估方法综述.
    物理学报, 72(24), 2023.

  • Kailong Zhao, Fang Liang, Yuhao Xia, Minghua Hou, Guijun Zhang.
    Recent advances in protein folding pathway prediction through computational methods.
    Current Medicinal Chemistry, 31(26): 4111-4126, 2024.

  • Jun Hu, Yuxuan Tang, Yu Zhou, Zhe Li, Bing Rao, Guijun Zhang.
    Improving DNA 6mA Site Prediction via Integrating Bidirectional Long Short-Term Memory, Convolutional Neural Network, and Self-Attention Mechanism.
    Journal of Chemical Information and Modeling, 2023.

  • Zhaohong Huang, Xinyue Cui, Yuhao Xia, Kailong Zhao, Guijun Zhang.
    Pathfinder: protein folding pathway prediction based on conformational sampling.
    PLOS Computational Biology, 19(9): e1011438, 2023.

  • Jun Liu, Dong Liu, Guangxing He, Guijun Zhang.
    Estimating protein complex model accuracy based on ultrafast shape recognition and deep learning in CASP15.
    PROTEINS: Structure, Function, and Bioinformatics, 91(12): 1861-1870, 2023.

  • Guangxing He, Jun Liu, Dong Liu, Guijun Zhang.
    GraphGPSM: a global scoring model for protein structure using graph neural networks.
    Briefings in Bioinformatics, 24(4): bbad219, 2023.

  • Jun Hu, Ming Dong, Yuxuan Tang, Guijun Zhang.
    Improving protein-protein interaction site prediction using deep residual neural network.
    Analytical Biochemistry, 115132, 2023.

  • Fengqi Ge, Chunxiang Peng, Xinyue Cui, Yuhao Xia, Guijun Zhang.
    Inter-domain distance prediction based on deep learning for domain assembly.
    Briefings in Bioinformatics, 24(3): bbad100, 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.

  • Jun Hu, Wenwu Zeng, Ningxin Jia, Muhammad Arif, Dongjun Yu, Guijun Zhang.
    Improving DNA-Binding protein prediction using three-part sequence-order feature extraction and a deep neural network algorithm.
    Journal of Chemical Information and Modeling, 63(3): 1044-1057, 2023.

2022

  • Jun Liu, Kailong Zhao, Guijun Zhang.
    Improved model quality assessment using sequence and structural information by enhanced deep neural networks.
    Briefings in Bioinformatics, 24(1): bbac507, 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.

  • 张贵军,侯铭桦, 彭春祥, 刘俊.
    多结构域蛋白质结构预测方法综述.
    电子科技大学学报(自科版), 51(06): 820-829, 2022.

  • 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.

  • 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. [Web Server]

  • 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. [Web Server]

  • 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. [Web Server]

  • Biao Zhang, Dong Liu, Yang Zhang, Hong-Bin Shen, Guijun Zhang.
    Accurate flexible refinement for atomic-level protein structure using cryo-EM density maps and deep learning.
    Briefings in Bioinformatics, 23(2): bbac026, 2022.

  • Qiongqiong Feng, Minghua Hou, Jun Liu, Kailong Zhao, Guijun Zhang.
    Construct a variable-length fragment library for de novo protein structure prediction.
    Briefings in Bioinformatics, 23(3): bbac086, 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.

  • 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.

  • Rao Liang, Ningxin Jia, Jun Hu, Dongjun Yu, Guijun Zhang.
    ATPdock: a template-based method for ATP-specific protein-ligand docking.
    Bioinformatics. 38(2), 556-558, 2022.

  • 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.

  • 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
  • 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.

  • 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.

  • 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.

  • 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 Hu, Liang Rao, Yiheng Zhu, Guijun Zhang, Dongjun Yu.
    TargetDBP+: Enhancing the performance of identifying DNA-binding proteins via weighted convolutional features.
    Journal of Chemical Information and Modeling, 61(1): 605-515, 2021

  • Jun Hu, Yansong Bai, Linlin Zheng, Ningxin Jia, Dongjun Yu, Guijun Zhang.
    Protein-DNA binding residue prediction via bagging strategy and sequence-based cube-format feature.
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, DOI: 10.1109/TCBB.2021.3123828, in press, 2021.

  • Xueqiang Fan, Jun Hu, Ningxin Jia, Dongjun Yu, Guijun Zhang.
    Improved protein relative solvent accessibility prediction using deep multi-view feature learning framework.
    Analytical Biochemistry, 631: 114358, 2021.

  • Jun Hu, Linlin Zhen, Yansong Bai, Kewen Zhang, Dongjun Yu, Guijun Zhang.
    Accurate prediction of protein-ATP binding residues using position-specific frequency matrix.
    Analytical Biochemistry, 626: 114241, 2021.

  • Liujing Wang, Xiaogen Zhou, Tengyu Xie, Jun Liu, Guijun Zhang.
    Adaptive Differential Evolution with Information Entropy-Based Mutation Strategy.
    IEEE Access, 9: 146783-146796, 2021.

  • 张贵军, 刘俊, 赵凯龙.
    基于片段组装的蛋白质结构预测方法综述.
    数据采集与处理, 36(4): 629-638, 2021.

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.

  • Yan Zhang, Yaru Zhang, Jun Hu, Ji Zhang, Fangjie Guo, Meng Zhou, Guijun Zhang, Fulong Yu, Jianzhong Su.
    scTPA: A web tool for single-cell transcriptome analysis of pathway activation signatures.
    Bioinformatics, 36(24): 4217-4219, 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.

  • 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.

  • Yongdong Wang, Dongwei Xu, Peng Peng, Qi Xuan, Guijun Zhang.
    An urban commuters' OD hybrid prediction method based on big GPS data.
    Chaos, 30(9): 093128-1~9, 2020.

  • Yongdong Wang, Dongwei Xu, Peng Peng, Guijun Zhang.
    Analysis of road travel behavior based on big trajectory data.
    IET Intelligent Transport Systems, 14(12): 1691-1703, 2020.

  • Jun Hu, Liang Rao, Xueqiang Fan, Guijun Zhang.
    Identification of ligand-binding residues using protein sequence profile alignment and query-specific support vector machine model.
    Analytical Biochemistry, 604: 1-8, 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.

  • 武楚雄, 陈驰, 张贵军.
    动态路网选址-路径优化算法及实现.
    控制理论与应用, 37(11): 2398-2412, 2020.

2019
  • 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. [Web 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.

  • Yongdong Wang, Dongwei Xu, Peng Peng, Guijun Zhang, Xuemei Xiao.
    Kernel PCA for road traffic data non-linear feature extraction.
    IET Intelligent Transport Systems, 13(8): 1291-1298, 2019.

  • Weifeng Chen, Yinyin Ren, Guijun Zhang, Lorenz T. Biegler.
    A simultaneous approach for singular optimal control based on partial moving grid.
    AIChE Journal, 65(6): e16584, 2019.

2012-2018
  • 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.

  • Yongdong Wang, Dongwei Xu, YunLu, Junyan Shen, Guijun Zhang.
    Compression algorithm of road traffic data in time series based on temporal correlation.
    IET Intelligent Transport Systems, 12(3): 177-185, 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.

  • Dongwei Xu, Yongdong Wang, Liming Jia, Guijun Zhang, Haifeng Guo.
    Compression Algorithm of Road Traffic Spatial Data Based on LZW Encoding.
    Journal of Advanced Transportation, 2017: 8182690, 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.

  • 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.

  • Xiaogen Zhou, Guijun Zhang, Xiaohu Hao. Li Yu.
    Enhanced differential evolution using local Lipschitz underestimate strategy for computationally expensive optimization problems.
    Applied Soft Computing, 48(11): 169-181, 2016.

  • 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.

  • 张贵军, 何洋军, 郭海锋, 冯远静, 徐建明.
    基于广义凸下界估计的多模态差分进化算法.
    软件学报, 24(6): 1177−1195, 2013.

  • 吴海涛, 张贵军, 洪榛, 俞立.
    进化树拓扑路网构建及多停靠点路径规划方法研究.
    计算机学报, 35(5): 964-971, 2012.