Jun Hu, Yan-Song Bai, Lin-Lin Zheng, Ning-Xin Jia, Dong-Jun Yu, Gui-Jun Zhang. Protein-DNA Binding Residue Prediction via Bagging Strategy and Sequence-based Cube-Format Feature [J]. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2021, xx(xx): xx. [DOI:10.1109/TCBB.2021.3123828] [Web Server]
Liang Rao, Ning-Xin Jia, Jun Hu#, Dong-Jun Yu#, and Gui-Jun Zhang#. ATPdock: a template-based method for ATP-specific protein–ligand docking [J]. Bioinformatics, 2021, 631: 114358. [DOI:10.1093/bioinformatics/btab667] [Web Server]
Xue-Qiang Fan, Jun Hu#, Ning-Xin Jia, Dong-Jun Yu#, and Gui-Jun Zhang#. Improved protein relative solvent accessibility prediction using deep multi-view feature learning framework [J]. Analytical Biochemistry, 2021, 631: 114358. [DOI:10.1016/j.ab.2021.114358] [Web Server]
Jun Hu, Lin-Lin Zheng, Yan-Song Bai, Ke-Wen Zhang, Dong-Jun Yu, and Gui-Jun Zhang. Accurate prediction of protein-ATP binding residues using position-specific frequency matrix [J]. Analytical Biochemistry, 2021, 626: 114241. [Download Citation with Endnote or BibTex Format] [DOI:10.1016/j.ab.2021.114241] [Web Server] (WOS: 000663454300003)
Jun Hu, Liang Rao, Yi-Heng Zhu, Gui-Jun Zhang, and Dong-Jun Yu. TargetDBP+: Enhancing the Performance of Identifying DNA-Binding Proteins via Weighted Convolutional Features [J]. Journal of Chemical Information and Modeling, 2021, 61(1): 505-515. [Download Citation with Endnote or BibTex Format] [DOI:10.1021/acs.jcim.0c00735] [Web Server] (WOS: 000613719400044)
Fang Ge, Jun Hu, Yiheng Zhu, Arif M, and Dongjun Yu. TargetMM: accurate missense mutation prediction by utilizing local and global sequence information with classifier ensemble. Combinatorial Chemistry & High Throughput Screening. 2020 [Download Citation with Endnote or BibTex Format] [DOI:10.2174/1386207323666201204140438] (PMID:33280588)
Jun Hu, Liang Rao, Xueqiang Fan, and Guijun Zhang. Identification of ligand-binding residues using protein sequence profile alignment and query-specific support vector machine model. Analytical Biochemistry. 2020, 604:113799 [Download Citation with Endnote or BibTex Format] [DOI:10.1016/j.ab.2020.113799] [Standalone Program] (WOS:000556551500012)
Yiheng Zhu, Jun Hu, Fang Ge, Fuyi Li, Jiangning Song, Yang Zhang, and Dongjun Yu. Accurate Multi-Stage Prediction of Protein Crystallization Propensity Using Deep-Cascade Forest with Sequence-Based Features. Briefings in Bioinformatics. 2021, 22(3):bbaa076. [Download Citation with Endnote or BibTex Format] [DOI:10.1093/bib/bbaa076] [No Web Server]
Yan Zhang, Yaru Zhang, Jun Hu, Ji Zhang, Fangjie Guo, Meng Zhou, Guijun Zhang, Fulong Yu, and Jianzhong Su. scTPA: A web tool for single-cell transcriptome analysis of pathway activation signatures. Bioinformatics. 2020, 36(4): 4217-4219. [Download Citation with Endnote or BibTex Format] [DOI:10.1101/2020.01.15.907592] [No Web Server](WOS:000583886000021)
Yiheng Zhu, Jun Hu, Yong Qi, XiaoNing Song, and Dongjun Yu. Boosting Granular Support Vector Machines for the Accurate Prediction of Protein-Nucleotide Binding Sites. Combinatorial Chemistry & High Throughput Screening. 2019, 22, 455-469 [DOI:10.2174/1386207322666190925125524] [No Web Server]
Xiaogen Zhou, Jun Hu, Chengxin Zhang, Guijun Zhang, and Yang Zhang. Assembling multi-domain protein structures through analogous global structural alignments. Proceedings of the National Academy of Sciences of the United States of America. 2019, 116: 15930-15938 [Download Citation with Endnote or BibTex Format] [DOI:10.1073/pnas.1905068116] [Web Server]
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. 2019, 18(4):567-577. [Download Citation with Endnote or BibTex Format] [DOI:10.1109/TNB.2019.2922101] [No Web Server](WOS:000498049700008)
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. 2021, 18(2):697-707. [Download Citation with Endnote or BibTex Format] [DOI:10.1109/TCBB.2019.2921958] [No Web Server](WOS:000638400100015)
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. 2020, 17(6):2119-2130. [Download Citation with Endnote or BibTex Format] [DOI:10.1109/TCBB.2019.2917452] [No Web Server](WOS:000597841800026)
Yang Li, Jun Hu, Chengxin Zhang, Dong-Jun Yu, and Yang Zhang. ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks. Bioinformatics. 2019, 35(2):4647-4655. [Download Citation with Endnote or BibTex Format] [DOI:10.1093/bioinformatics/btz291] [Web Server](WOS:000501728500014)
Yi-Heng Zhu, Jun Hu, Xiao-Ning Song, Dong-Jun Yu. DNAPred: accurate identification of DNA-binding sites from protein sequence by ensembled hyperplane-distance-based support vector machines. Journal of Chemical Information and Modeling. 2019, 59(6):3057-3071. [Download Citation with Endnote or BibTex Format] [DOI:10.1021/acs.jcim.8b00749] [Web Server](WOS:000473116500050)
Jun Hu, Xiao-Gen Zhou, Yi-Heng Zhu, Dong-Jun Yu, Guijun Zhang. TargetDBP: Accurate DNA-Binding Protein Prediction via Sequence-based Multi-View Feature Learning. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2020, 17(4):1419-1429. [In Press] [Download Citation with Endnote or BibTex Format] [DOI:10.1109/TCBB.2019.2893634] [Web Server](WOS:000556777900029)
Jun Hu, Zi Liu, Dong-Jun Yu, and Yang Zhang. LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening [J]. Bioinformatics, 2018, 34(13): 2209-2218. [Download Citation with Endnote or BibTex Format] [DOI:10.1093/bioinformatics/bty081] [Web Server] (WOS:000438247800073) (PubMed ID: 29462237)
Jun Hu, Yang Li, Yang Zhang, and Dong-Jun Yu. ATPbind: accurate protein-ATP binding site prediction by combining sequence-profiling and structure-based comparisons [J]. Journal of Chemical Information and Modeling, 2018, 58(2): 501-510. [Download Citation with Endnote or BibTex Format] [DOI:10.1021/acs.jcim.7b00397] [Web Server] (WOS: 000426613800029)
Jun Hu, Yang Li, Ming Zhang, Xibei Yang, Hong-Bin Shen, and Dong-Jun Yu. Predicting Protein-DNA Binding Residues by Weightedly Combining Sequence-based Features and Boosting Multiple SVMs [J]. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017, 14(6): 1389-1398. [Download Citation with Endnote or BibTex Format] [DOI:10.1109/TCBB.2016.2616469] [Web Server] [Dataset] (WOS: 000418112400017)
Jun Hu, Ke Han, Yang Li, Jing-Yu Yang, Hong-Bin Shen, and Dong-Jun Yu. TargetCrys: protein crystallization prediction by fusing multi-view features with two-layered SVM [J]. Amino Acids, 2016, 48(11): 2533-2547. [Download Citation with Endnote or BibTex Format] [DOI] [Web Server] (WOS: 000386691700005)
Jun Hu, Yang Li, Wu-Xia Yan, Jing-Yu Yang, Hong-Bin Shen, and Dong-Jun Yu. KNN-based Dynamic Query-Driven Sample Rescaling Strategy for Class Imbalance Learning [J]. Neurocomputing, 2016, 191: 363-373. [Download Citation with Endnote or BibTex Format] [DOI] [Web Server] (WOS: 000375165900031)
Jun Hu, Yang Li, Jing-Yu Yang, Hong-Bin Shen, and Dong-Jun Yu. GPCR-drug Interactions Prediction Using Random Forest with Drug-Association-Matrix-Based Post-Processing Procedure [J]. Computational Biology and Chemistry, 2016, 60: 59-71. [Download Citation with Endnote or BibTex Format] [DOI] [Web Server] (WOS: 000369678300007)
Wuxia Yan, Sheng Wang, Jun Hu, and Chuancai Liu. Fronto-parallel building facades stitching. Electronics Letters, 2016, 52(18): 1524-1526. (WOS: 000383378500010)
Xue He, Ke Han, Jun Hu, Hui Yan, Jing-Yu Yang, Hong-Bin Shen, and Dong-Jun Yu. TargetFreeze: Identifying Antifreeze Proteins via a Combination of Weights using Sequence Evolutionary Information and Pseudo Amino Acid Composition. Journal of Membrane Biology, 2015, 248(6): 1005-1014. [Download Citation with Endnote or BibTex Format] [DOI] [Web Server] (WOS: 000363265100007)
Dong-Jun Yu, Jun Hu, Qian-Mu Li, Zhen-Min Tang, Jing-Yu Yang, and Hong-Bin Shen. Constructing Query-Driven Dynamic Machine Learning Model with Application to Protein-Ligand Binding Sites Prediction. IEEE Transactions on NanoBioscience, 2015, 14(1): 45-58. [Web Server] (WOS: 000350884300006)
Dong-Jun Yu, Yang Li, Jun Hu, Xibei Yang, Jing-Yu Yang, and Hong-Bin Shen. Disulfide Connectivity Prediction Based on Modelled Protein 3D Structural Information and Random Forest Regression. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2015, 12(3): 611-621. [Web Server] (WOS: 000356608100013)