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1 Xinxin Song#, Zhuan Zhou#, Hongchun Li#, Yifan Xue, Ziyi Fu, Xinhua Lu, Ivet Bahar, Oliver Kepp, Mien-Chie Hung, Guido Kroemer and Yong Wan. Pharmacological suppression of B7-H4 glycosylation restores antitumor immunity in immune-cold breast cancers. Cancer Discovery. 2020
2 Bentley Wingert#, James M. Krieger#, Hongchun Li and Ivet Bahar. Adaptability and Specificity: How do proteins balance opposing needs to achieve function? Current Opinion in Structural Biology. 2021, 67: 25-32
3 Ke Liu#, Rongfeng Zou#, Wenqiang Cui#, Meiqing Li#, Xueying Wang, Junlin Dong, Hongchun Li, Hongpei Li, Peihui Wang, Ximing Shao, Wu Su, H. C. Stephen Chan, Hongchang Li, and Shuguang Yuan. Clinical HDAC inhibitors are effective drugs to prevent the entry of SARS-CoV2. ACS Pharmacology & Translational Science. 2020
4 Hongchun Li#, Fen Pei#, D. Lansing Taylor and Ivet Bahar. QuartataWeb: integrated chemical-protein-pathway mapping for polypharmacology and chemogenomics. Bioinformatics. 2020, 36(12): 3935–3937.
5 Hongchun Li#, Pemra Doruker#, Guang Hu and Ivet Bahar. Modulation of Toroidal Proteins Dynamics in Favor of Functional Mechanisms upon Ligand Binding. Biophysical Journal. 2020, 118(7): 1782-1794.
6 Jiyoung Lee#, James M. Krieger#, Hongchun Li and Ivet Bahar. Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations. Protein Science. 2020, 29, 76-86
7 Yan Zhang, Pemra Doruker, Burak Kaynak, She Zhang, James M. Krieger, Hongchun Li and Ivet Bahar. Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior. Current Opinion in Structural Biology. 2020, 62:14–21.
8 Xiaoyan Zhuang#, Aihui Zhang#, Siyao Qiu, Chun Tang, Shiqiang Zhao, Hongchun Li, Yonghui Zhang, Yali Wang, Binju Wang, Baishan Fang and Wenjing Hong. Coenzyme coupling boosts charge transport through single bioactive enzyme junctions. iScience. 2020. 23(4): 101001.
9 Junlong Chi#, Hongchun Li#, Zhuan Zhou, Javier Izquierdo-Ferrer, Yifan Xue, Cindy M. Wavelet, Gary E. Schiltz, Xinghua Lu, Ivet Bahar and Yong Wan. A Novel Strategy to Block Mitotic Progression for Targeted Therapy. EBioMedicine. 2019, 49, 40-54.
10 She Zhang#, Hongchun Li#, James M. Krieger# and Ivet Bahar. Shared signature dynamics tempered by local fluctuations enables fold adaptability and specificity. Molecular Biology and Evolution. 2019, 36(9):2053–2068.
11 Fen Pei#, Hongchun Li#, Bing Liu and Ivet Bahar. Quantitative systems pharmacological analysis highlights the pleiotropic nature of proteins targeted by drugs of abuse. Frontiers in Pharmacology. 2019, 10: 191.
12 Karolina Mikulska-Ruminska#, Indira Shrivastava#, James M. Krieger, She Zhang, Hongchun Li, Hülya Bayır, Sally E. Wenzel, Andrew P. VanDemark, Valerian E. Kagan and Ivet Bahar. Characterization of differential dynamics, specificity, and allostery of lipoxygenase family members. Journal of Chemical Information and Modeling. 2019, 59(5): 2496-2508.
13 Hongchun Li#, Yuan-Yu Chang#, Jiyoung Lee, Ivet Bahar and Lee-Wei Yang. DynOmics: dynamics of structural proteome and beyond. Nucleic Acids Research, 2017, 45: W374-W380.
14 Hongchun Li#, Nanaocha Sharma#, Ignacio J. General, Gideon Schreiber and Ivet Bahar. Dynamic Modulation of Binding Affinity as a Mechanism for Regulating Interferon Signaling. Journal of Molecular Biology, 2017, 429(16): 2571-2589.
15 Fen Pei, Hongchun Li, Mark J. Henderson, Steven A. Titus, Ajit Jadhav, Anton Simeonov, Murat Can Cobanoglu, Seyed H. Mousavi, Tongying Shun, Lee McDermott, Prema Iyer, Michael Fioravanti, Diane Carlisle, Robert M. Friedlander, Ivet Bahar, D. Lansing Taylor, Timothy R. Lezon, Andrew M. Stern & Mark E. Schurdak. Connecting neuronal cell protective pathways and drug combinations in a Huntington’s disease model through the application of quantitative systems pharmacology. Scientific Reports, 2017, 7: 17803.
16 Hongchun Li, Yuan-Yu Chang, Lee-Wei Yang and Ivet Bahar. iGNM 2.0: The Gaussian Network Model Database for Biomolecular Structural Dynamics. Nucleic Acids Research. 2016, 44(D1): D415-D422.
17 Chin-Chi Chang, Md. Imran Khan, Kun-Lin Tsai, Hongchun Li, Lee-Wei Yang, Ruey-Hwang Chou, and Chin Yu. Blocking the interaction between S100A9 and RAGE V domain using CHAPS molecule: A novel route to drug development against cell proliferation. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 2016, 1864(11): 1558-1569.
18 Hongchun Li#, Shun Sakuraba#, Aravind Chandrasekaran and Lee-Wei Yang. Molecular binding sites are located near the interface of intrinsic dynamics domains (IDDs). Journal of Chemical Information and Modeling. 2014, 54(8): 2275-2285.
19 Jhen-Kai Li, Jiahn-Haur Liao, Hongchun Li, Chiao-I Kuo, Kai-Fa Huang, Lee-Wei Yang, Shih-Hsiung Wu and Chung-I Chang. The N-terminal substrate-recognition domain of a LonC protease exhibits structural and functional similarity to cytosolic chaperones. Acta Crystallographica Section D: Biological Crystallography. 2013, 69: 1789-1797.
20 Arun A. Gupta, Ruey-Hwang Chou, Hongchun Li, Lee-Wei Yang, Chin Yu. Structural insights into the interaction of human S100B and basic fibroblast growth factor (FGF2): Effects on FGFR1 receptor signaling. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 2013, 1834(12): 2606-2619.
21 Guangya Zhang, Zhishan Chen, Hongchun Li and Kaizong Huang. Molecular dynamic simulation of elastin-like peptide. Computers and Applied Chemistry. 2011, 28(4): 399-402.
22 Huihua Ge, Hongchun Li, Guangya Zhang. Homology Modeling and Molecular Dynamic Simulation of Xylanase from Bacillus pumilus. Journal of Huaqiao University. 2011, 32(03): 296-299.
23 Hongchun Li, Guangya Zhang and Baishan Fang. Using Pseudo Amino Acid Composition to Predict Hydrolase Subfamily. Journal of Huaqiao University. 2010, 31(3): 317-321.
24 Guangya Zhang, Hongchun Li, Jiaqiang Gao and Baishan Fang. Protein piezophilicity: Solvent accessibility-based difference of amino acid in adaptation of proteins to high hydrostatic pressure. Acta Microbiologica Sinica. 2010, 50(5): 621-627.
25 Guangya Zhang, Hongchun Li and Baishan Fang. Discriminating acidic and alkaline enzymes using a random forest model with secondary structure amino acid composition. Process Biochemistry. 2009, 44(6): 654-660.
26 Guangya Zhang, Hongchun Li, Jiaqiang Gao and Baishan Fang. Influence of amino acid and dipeptide composition on protein stability of piezophilic microbes. Acta Microbiologica Sinica. 2009, 49(2): 198-203.
27 Guangya Zhang, Hongchun Li, Jiaqiang Gao and Baishan Fang. Predicting Lipase Types by Improved Chou's Pseudo-Amino Acid Composition. Protein and Peptide Letters. 2008, 15(10): 1132-1137.
28 Guangya Zhang, Hongchun Li and Baishan Fang. Predicting the Cofactors of Oxidoreductases by the Modified Pseudo-amino Acid Composition. Chinese Journal of Biotechnology. 2008, 24(8): 1439-1445.
29 Guangya Zhang, Hongchun Li, Jiaqiang Gao and Baishan Fang. Prediction of lipases types by different scale pseudo-amino acid composition. Chinese Journal of Biotechnology. 2008, 24(11): 1968-74.
30 Guangya Zhang, Hongchun Li and Baishan Fang*. Prediction of protein thermostability with a k-nearest neighbors algorithm. Computers and Applied Chemistry. 2008, 25(1): 39-41.