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科研

2020

1. Zhongwen Chen, Yuhong Cao, Chun-Wei Lin, Steven Alvarez, Dongmyung Oh, Peidong Yang*, Jay T. Groves*. Nanopore mediated protein delivery enabling 3-color single molecule tracking in living cells. PNAS, in press.

2. Joyce J. Wong, Zhongwen Chen, Jean K. Chung|, Jay T. Groves*, Theodore S. Jardetzky*, EphrinB2 clustering by Nipah virus G is required to activate and trap F intermediates at supported lipid bilayer-cell interfaces. Science Advances, in press.

3. Gang Xu, Qinghua Wang, Jianpeng Ma*. OPUS-Refine: A Fast Sampling-Based Framework for Refining Protein Backbone Torsion Angles and Global Conformation, Journal of Chemical Theory and Computation, 2020, 16 (2) , 1359-1366. 

4.  Gang Xu, Qinghua Wang, Jianpeng Ma*. OPUS-Fold: An Open-Source Protein Folding Framework Based on Torsion-Angle Sampling, Journal of Chemical Theory and Computation, 2020, 16 (6), 3970-3976. https://doi.org/10.1021/acs.jctc.0c00186

5. Rongying Liu, Zdravko Kochovski, Long Li, Yue-wen Yin, Jing Yang, Guang Yang, Guoqing Tao, Anqiu Xu, Ensong Zhang, Hong-ming Ding*, Yan Lu*, Guosong Chen*, Ming Jiang, Fabrication of Pascal-triangle Lattice of Proteins by Inducing Ligand Strategy, Angew. Chem. Int. Ed., 2020, 59, 9617. DOI:10.1002/anie.202000771

6. Jing Yang, Qiqige Du, Long Li, Tingting Wang, Yingle Feng, Mu-Ping Nieh, Juzheng Sheng,* Guosong Chen*, Glycosyltransferase-Induced Morphology Transition of Glycopeptide Self-Assemblies with Proteoglycan ResiduesACS Macro Lett., 2020, 9, 929-936. pubs.acs.org/doi/10.1021/acsmacrolett.0c00306

7. Jingwei Weng, Wenning Wang*, Dynamic Multivalent Interactions of Intrinsically Disordered Proteins Curr. Opin. Struct. Biol. 62:9-13 (2020). doi: 10.3390/biom9030081.

8. Menghua Song, Gan Li, Qi Zhang, Jianping Liu, Qiang Huang*, De novo post-SELEX optimization of a G-quadruplex DNA aptamer binding to marine toxin gonyautoxin 1/4, Computational and Structural Biotechnology Jornal, 2020 (18):3425-3433, https://doi.org/10.1016/j.csbj.2020.10.041


2019

1. Gang Xu, Tianqi Ma, Junqing Du, Qinghua Wang, and Jianpeng MaOPUS-Rota2: An Improved Fast and Accurate Side-Chain Modeling Method. Journal of Chemical Theory and Computation, 2019 155154-5160DOI: 10.1021/acs.jctc.9b00309.

2. Gang Xu, Zhigang Song, Zhuo Sun, Calvin Ku, Zhe Yang, Cancheng Liu, Shuhao Wang, Jianpeng Ma, and Wei Xu, CAMEL: A Weakly Supervised Learning Framework for Histopathology Image Segmentation, Proceedings of the IEEE International Conference on Computer Vision, 2019.

3. Chunhua Liu, Zelin Shan, Jianqiao Diao, Wenyu Wen*, Wenning Wang*, Crystal structure of the coiled-coil domain of Drosophila TRIM protein Brat. Proteins, 2019 87(8): 706-710 doi:10.1002/prot.25691.

4. Dongdong Wang, Jingwei Weng*, Wenning Wang*, Glycerol transport through the aquaglyceroporin GlpF: bridging dynamics and kinetics with atomic simulation, Chemical Science 2019 10(29): 6957-6965 doi:10.1039/c9sc01690b.

5. Dongdong Wang, Jingwei Weng*, Wenning Wang*, An unconventional ligand-binding mechanism of substrate-binding proteins: MD simulation and Markov state model analysis of BtuF, Journal of Computational Chemistry 2019 40(14): 1440-1448 doi:10.1002/jcc.25798.

6. Dongdong Wang, Wenning Wang*, Extreme Fuzziness: Direct Interactions between Two IDPs, Biomolecules 2019 9(3) doi:10.3390/biom9030081.

7. Jingwei Weng, Wenning Wang*, Structural Features and Energetics of the Periplasmic Entrance Opening of the Outer Membrane Channel TolC Revealed by Molecular Dynamics Simulation and Markov State Model Analysis, Journal of Chemical Information and Modeling , 2019 59(5): 2359-2366 doi:10.1021/acs.jcim.8b00957.

8. Ruijie YaoJiaqiang QianQiang Huang*, Deep-learning with synthetic data enables automated picking of cryo-EM particle images of biological macromolecules, Bioinformatics, 2019doi:10.1093/bioinformatics/btz728.


2018

1. Chunhua Liu, Jinwei Weng, Dan Wang, Maohua Yang, Min Jia, and Wenning Wang*, A Residue outside the Binding Site Determines the G alpha Binding Specificity of GoLoco Motifs. Biochemistry 2018 57(47): 6562-6569 doi:10.1021/acs.biochem.8b00848

2. Shaowen Wu, Dongdong Wang, Jingwei Weng, Jianwei Liu*, Wenning Wang*, A revisit of the conformational dynamics of SNARE protein rYkt6, Biochemical and Biophysical Research Communications 2018 503(4): 2841-2847 doi:10.1016/j.bbrc.2018.08.052.