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Jun Liu, Dong Liu, Guijun Zhang.
DeepUMQA3: a web server for accurate assessment of interface residue accuracy in protein complexes.
Bioinformatics, In press, 2023. -
Haitao Zhu, Yuhao Xia, Guijun Zhang.
E2EDA: Protein domain assembly based on end-to-end deep learning.
Journal of Chemical Information and Modeling, In press, 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, 录用, 2023. -
Kailong Zhao, Fang Liang, Yuhao Xia, Minghua Hou, Guijun Zhang.
Recent advances in protein folding pathway prediction through computational methods.
Current Medicinal Chemistry, in press, 2023. -
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, in press, 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, 2023. -
Guangxing He, Jun Liu, Dong Liu, Guijun Zhang.
GraphGPSM: a global scoring model for protein structure using graph neural networks.
Briefings in Bioinformatics, 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, 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.
-
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, 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.
Information entropy-based mutation strategy adaptive differential evolution.
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.