Publications

These are the papers we published.

1, Wenzhi Mao#, Tong Wang, Wenxuan Zhang, and Haipeng Gong*, “Identification of residue pairing in interacting β-strands from a predicted residue contact map”, BMC Bioinformatics, 19(1): 146, DOI: 10.1186/s12859-018-2150-1, 2018.

2, Wenze Ding#,Wenzhi Mao#, Di Shao#, Wenxuan Zhang and Haipeng Gong*,“DeepConPred2: an improved method for the prediction of protein residue contacts”, Computational and Structural Biotechnology Journal,16:503-510,2018.

3, Juanrong Zhang#, Wenzhi Mao#, Yanhui Ren#, Rui-Ning Sun, Nieng Yan*, and Haipeng Gong*, “Simulating the ion permeation and ion selection for a eukaryotic voltage-gated sodium channel NavPaS”, Protein & Cell, 9(6): 580-585, 2018.

4, Dapeng Xiong#, Wenzhi Mao#, and Haipeng Gong*, “Predicting the helix-helix interactions from correlated residue mutations”, Proteins: Structure, Function and Bioinformatics, 85(12): 2162-2169, 2017.

5, Meng Ke#, Yafei Yuan, Xin Jiang, Nieng Yan*, and Haipeng Gong*, “Molecular determinants for the thermodynamic and functional divergence of uniporter GLUT1 and proton symporter XylE”, PLoS Computational Biology, 13(6): e1005603, 2017.

6, Dapeng Xiong#, Jianyang Zeng*, and Haipeng Gong*, “A deep learning framework for improving long-range residue-residue contact prediction using a hierarchical strategy”, Bioinformatics, 33(17): 2675-2683, 2017.

7, Ruining Sun# and Haipeng Gong*, “Simulating the activation of voltage sensing domain for a voltage-gated sodium channel using polarizable force field”, Journal of Physical Chemistry Letters, 8: 901-908, 2017.

8, Yang Li#, Ruining Sun#, Huihui Liu, and Haipeng Gong*, “Molecular dynamics study of ion transport through an open model of voltage-gated sodium channel”, Biochimica et Biophysica Acta – Biomembranes, 1859(5): 879-887, 2017.

9, Tong Wang#, Yuedong Yang, Yaoqi Zhou, and Haipeng Gong*, “LRFragLib: an effective algorithm to identify fragments for de novo protein structure prediction”, Bioinformatics, 33(5): 677-684, 2017.

10, Xiaoying Lv#, Hao Liu, Haifeng Chen, and Haipeng Gong*, “Coupling between ATP hydrolysis and protein conformational change in maltose transporter”, Proteins: Structure, Function and Bioinformatics, 85(2): 207-220, 2017.

11, Liling Xu#, Mengdie Xia#, Jun Guo#, Xiaolin Sun#, Hua Li, Chenguang Xu, Xiaomei Gu, Haowen Zhang, Junyang Yi, Yan Fang, Hengyi Xie, Jing Wang, Zhixun Shen, Boxin Xue, Yujie Sun, Tobias Meckel, Ying-Hua Chen, Zhibin Hu, Zhanguo Li*, Chenqi Xu*, Haipeng Gong*, and Wanli Liu*, “Impairment on the lateral mobility induced by structural changes underlies the functional deficiency of the lupus-associated polymorphism FcγRIIB-T232”, Journal of Experimental Medicine, 213(12): 2707-2727, 2016.

12, Yang Li#, Huihui Liu#, Mengdie Xia, and Haipeng Gong*, “Lysine and the Na+/K+ selectivity in mammalian voltage-gated sodium channels”, PLoS One, 11(9): e0162413, 2016.

13, Huihui Liu#, Yan-Song Gao#, Xiang-Jun Chen, Zhe Chen, Hai-Meng Zhou, Yong-Bin Yan*, and Haipeng Gong*, “A single residue substitution accounts for the significant difference in thermostability between two isoforms of human cytosolic creatine kinase”, Scientific Reports, 6: 21191, 2016.

14, Yufeng Liu#, Meng Ke, and Haipeng Gong*, “Protonation of Glu135 facilitates the outward-to-inward structural transition of fucose transporter”, Biophysical Journal, 109(3): 542-551, 2015.

15, Dapeng Xiong#, Jianyang Zeng, and Haipeng Gong*, “RBRIdent: an algorithm for improved identification of RNA-binding residues in proteins from primary sequences”, Proteins: Structure, Function and Bioinformatics, 83(6):1068-1077, 2015.

16, Yang Li# and Haipeng Gong*, “Theoretical and simulation studies on voltage-gated sodium channels”, Protein & Cell, 6(6): 413-422, 2015.

17, Yufeng Liu#, Jianyang Zeng, and Haipeng Gong*, “Improving the orientation-dependent statistical potential using a reference state”, Proteins: Structure, Function and Bioinformatics, 82(10): 2383-2393, 2014.

18, Xiaoying Lv#, Huihui Liu, Meng Ke, and Haipeng Gong*, “Exploring the pH-dependent substrate transport mechanism of FocA using molecular dynamics simulation”, Biophysical Journal, 105(12): 2714-2723, 2013.

19, Yufeng Liu#, Esmael Haddadian, Tobin R. Sosnick, Karl F. Freed*, and Haipeng Gong*, “A novel implicit solvent model for simulating the molecular dynamics of RNA”, Biophysical Journal, 105(5): 1248-1257, 2013.

20, Mengdie Xia#, Huihui Liu#, Yang Li#, Nieng Yan, and Haipeng Gong*, “The mechanism of Na+/K+ selectivity in mammalian voltage-gated sodium channels based on molecular dynamics simulation”, Biophysical Journal, 104(11): 2401-2409, 2013.

21, Xu Zhang#, Mengdie Xia#, Yang Li#, Huihui Liu#, Xin Jiang, Wenlin Ren, Jianping Wu, Paul DeCaen, Feng Yu, Sheng Huang, Jianhua He, David E. Clapham, Nieng Yan, and Haipeng Gong*, “Analysis of the selectivity filter of the voltage-gated sodium channel NavRh”, Cell Research, 23(3): 409-422, 2013.

22, Yufeng Liu# and Haipeng Gong*, “Using the unfolded state as the reference state improves the performance of statistical potentials”, Biophysical Journal, 103(9): 1950-1959, 2012.

23, Haipeng Gong#*, Lauren L. Porter, and George D. Rose*, “Counting peptide-water hydrogen bonds in unfolded proteins”, Protein Science, 20(2): 417-427, 2011.

24, Haipeng Gong#* and Karl F. Freed*, “Electrostatic solvation energy for two oppositely charged ions in a solvated protein system: salt bridges can stabilize proteins”, Biophysical Journal, 98(3): 470-477, 2010.