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Papers in reverse chronological order
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Journal Papers:
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2024
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[30] Zhen Cao, Lei Lei, Ziyun Zhou, Shimeng Xu, Linlin Wang, Weikang Gong, Qi Zhang, Bin Pan, Gaoxin Zhang, Quan Yuan, Liujuan Cui, Min Zheng, Tao Xu, You Wang, Shuyan Zhang, Pingsheng Liu
Apolipoprotein A-IV and its derived peptide, T55−121, improve glycemic control and increase energy expenditure.
Life Metabolism, 3: 1-12 (2024).
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2023
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[29] Shuang Yang, Weikang Gong, Tong Zhou, Xiaohan Sun, Lei Chen, Wenxue Zhou, Chunhua Li
emPDBA: protein-DNA binding affinity prediction by combining features from binding partners and interface learned with ensemble regression model.
Briefings in Bioinformatics, 24: 1-8 (2023).
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[28] Yanpeng Zhao, Jingjing Wang, Fubin Chang, Weikang Gong, Yang Liu, Chunhua Li
Identification of metal ion-binding sites in RNA structures using deep learning method.
Briefings in Bioinformatics, 24: 1-9 (2023).
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2022
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[27] Zhongjie Han, Zhixiang Wu, Weikang Gong, Wenxue Zhou, Lei Chen, Chunhua Li
Allosteric mechanism for SL RNA recognition by polypyrimidine tract binding protein RRM1: An atomistic MD simulation and network-based study.
International Journal of Biological Macromolecules, 221: 763-772 (2022).
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[26] Lei Chen, Weikang Gong, Zhongjie Han, Wenxue Zhou, Shuang Yang, Chunhua Li
Key residues in δ opioid receptor allostery explored by elastic network model and complex network model combined with perturbation method.
Journal of Chemical Information and Modeling, 62: 6727-6738 (2022).
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[25] Weikang Gong, JunJie Wee, Min-Chun Wu, Xiaohan Sun, Chunhua Li, Kelin Xia (First and Co-corresponding author)
Persistent spectral simplicial complex-based machine learning for chromosomal structural analysis in cellular differentiation.
Briefings in Bioinformatics, 23: 1-11 (2022).
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[24] Lei Chen, Weikang Gong, Chunhua Li
Dynamics and key residues of δ opioid receptor investigated by anisotropic network model.
Progress in Biochemistry and Biophysics, 49: 1146-1154 (2022).
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[23] Wenxue Zhou, Zhongjie Han, Zhixiang Wu, Weikang Gong, Shuang Yang, Lei Chen, Chunhua Li
Specific recognition between YTHDF3 and m6A-modified RNA: an all-atom molecular dynamics simulation study.
Proteins: Structure, Function, and Bioinformatics, 90: 1965-1972 (2022).
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[22] Tong Zhou, Jie Rong, Yang Liu, Weikang Gong, Chunhua Li
An ensemble approach to predict binding hotspots in protein-RNA interactions based on SMOTE data balancing and random grouping feature selection strategies.
Bioinformatics, 38: 2452-2458 (2022).
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[21] Hongwu Li, Weikang Gong (Co-first author and Corresponding author)
Study of allosteric transitions of human P-Glycoprotein by using the two-state anisotropic network model.
Frontiers in Medicine, 9: 815355 (2022).
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[20] Hao Chen, Weikang Wu, Jiaojiao Zhu, Zhengning Yang, Weikang Gong, Weibo Gao, Shengyuan A. Yang, Lifa Zhang
Chiral phonon diode effect in chiral crystals.
Nano Letters, 22: 1688-1693 (2022).
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[19] Shan Zhang, Weikang Gong, Na Zhang, Chunhua Li
Study on functionally dynamic features of human secretory phospholipase A2-IIA.
Progress in Biochemistry and Biophysics, 49: 1318-1324 (2022).
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[18] Xueqing Deng, Shihao Wang, Zhongjie Han, Weikang Gong, Yang Liu, Chunhua Li
Dynamics of binding interactions of TDP-43 and RNA：An equally weighted multiscale elastic network model study.
Proteins: Structure, Function, and Bioinformatics, 90: 589-600 (2022).
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2021
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[17] Weikang Gong, Aysam Guerler, Chengxin Zhang, Elisa Warner, Chunhua Li, Yang Zhang
Integrating multimeric threading with high-throughput experiments for structural interactome of Escherichia Coli.
Journal of Molecular Biology, 433: 166944 (2021)
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[16] Weikang Gong, Yang Liu, Yanpeng Zhao, Shihao Wang, Zhongjie Han, Chunhua Li
Equally weighted multiscale elastic network model and its comparison with traditional and parameter-free models.
Journal of Chemical Information and Modeling, 61: 921-937 (2021).
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[15] Xueqing Deng, Shihao Wang, Weikang Gong, Chunhua Li
Study on the interacting dynamics and key residues between human TDP-43 and DNA based on GNM model.
Progress in Biochemistry and Biophysics, 48: 1493-1500 (2021).
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[14] Yanpeng Zhao, Weikang Gong, Yang Liu, Jingjing Wang, Chunhua Li
Prediction of magnesium binding sites in RNA structures based on three-dimensional convolutional neural network.
Beijing Biomedical Engineering, 40: 570-576 (2021).
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[13] Qi Shao, Zhongjie Han, Jingmin Cheng, Qiankun Wang, Weikang Gong, Chunhua Li
Allosteric mechanism of human mitochondrial phenylalanyl-tRNA synthetase: an atomistic MD simulation and a mutual information-based network study.
The Journal of Physical Chemistry B, 125: 7651-7661 (2021).
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[12] Shan Zhang, Weikang Gong, Zhongjie Han, Yang Liu, Chunhua Li
Insight into shared properties and differential dynamics and specificity of secretory Phospholipase A2 family members.
The Journal of Physical Chemistry B, 125: 3353-3363 (2021).
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[11] Jingjing Wang, Yanpeng Zhao, Weikang Gong, Yang Liu, Mei Wang, Xiaoqian Huang, Jianjun Tan
EDLMFC: an ensemble deep learning framework with multi-scale features combination for ncRNA-protein interaction prediction.
BMC Bioinformatics, 22: 133 (2021).
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[10] Yang Liu, Weikang Gong, Zhen Yang, Chunhua Li
SNB-PSSM: A spatial neighbor based PSSM used for protein-RNA binding site prediction.
Journal of Molecular Recognition, e2887 (2021).
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[9] Yang Liu, Weikang Gong, Yanpeng Zhao, Xueqing Deng, Shan Zhang, Chunhua Li
aPRBind: protein-RNA interface prediction by combining sequence and I-TASSER model-based structural features learned with convolutional neural networks.
Bioinformatics, 37: 937-942 (2021).
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2020
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[8] Qi Shao, Weikang Gong, Chunhua Li (Co-first author)
A study on allosteric communication in U1A-snRNA binding interactions: network analysis combined with molecular dynamics data.
Biophysical Chemistry, 264: 106393 (2020).
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[7] Shihao Wang, Weikang Gong, Xueqing Deng, Yang Liu, Chunhua Li
Exploring the dynamics of RNA molecules with multiscale Gaussian network model.
Chemical Physics, 538: 110820 (2020).
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[6] Qurat ul Ain Farooq, Zeeshan Shaukat, Tong Zhou, Sara Aiman, Weikang Gong, Chunhua Li
Inferring Virus-Host relationship between HPV and its host Homo sapiens using protein interaction network.
Scientific Reports, 10: 8719 (2020).
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[5] Zhen Yang, Xueqing Deng, Yang Liu, Weikang Gong, Chunhua Li
Analyses on clustering of the conserved residues at protein-RNA interfaces and its application in binding site identification.
BMC Bioinformatics, 21: 57 (2020).
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2019
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[4] Shuping Cheng, Lu Zhang, Jianjun Tan, Weikang Gong, Chunhua Li, Xiaoyi Zhang
DM-RPIs: Predicting ncRNA-protein interactions using stacked ensembling strategy.
Computational Biology and Chemistry, 83: 107088 (2019).
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[3] Zhongjie Han, Qi Shao, Weikang Gong, Shihao Wang, Jiguo Su, Chunhua Li, Yang Zhang
Interpreting the dynamics of binding interactions of snRNA and U1A using a coarse-grained model.
Biophysical Journal, 116: 1625-1636 (2019).
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[2] Yue Zhang, Weikang Gong, Yan Wang, Yang Liu, Chunhua Li
Exploring movement and energy in human P-glycoprotein conformational rearrangement.
Journal of Biomolecular Structure and Dynamics, 37: 1104-1119 (2019).
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2017
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[1] Dashuai Lv, Weikang Gong, Yue Zhang, Yang Liu, Chunhua Li
A coarse-grained method to predict the open-to-closed behavior of glutamine binding protein.
Chemical Physics, 493: 166-174 (2017).
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Conference Papers:
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