Publication

Selected publications: 

(# for first authors, and * for corresponding authors)

  1. Prophage Activation: An In Silico Platform for Identifying Prophage Regulatory Elements to Inform Phage Engineering Against Drug-Resistant Bacteria. Saher Musrrat#, Zequan Han, Kai Wang, Yunhai Huang, Yanhui Xiang*,  Sen Liu*, Yen Yin*.
    • Life, 2025, 15(9): 1417.
  2. SUMO E1 covalent allosteric inhibitors modulate polyamine synthesis via the MAT2A-AdoMetDC axis. Shuai Zhang#, Jinzhu Li, Zhiying Wang, Yutong Jiao, Xiaoyu Shi, Yuanbao Ai, Juanping Wang, Sen Liu*. 
    • Bioorganic Chemistry, 2025, 164: 108930.
  3. Regulation Mechanism of Eukaryotic Translation Initiation Factor 5A in Epithelial-mesenchymal Transition. Canming Peng#, Juanping Wang, Sen Liu*.
    • Progress in Biochemistry and Biophysics, 2025, 52(8): 2018-2032.
  4. Tumor Microenvironment Polyamines Inhibit T Cell Antitumor Activity. Yuanbao Ai#, Xuemei Huang#, Sen Liu*.
    • Progress in Biochemistry and Biophysics, 2025, 52(8): 1986-1997.
  5. High-efficiency discovery and structure-activity-relationship analysis of non-substrate-based covalent inhibitors of S-adenosylmethionine decarboxylase. Yuanbao Ai#, Siyu Xu#, Yan Zhang#, Zhaoxiang Liu, Sen Liu*.
    • Journal of Medicinal Chemistry, 2025, 68(15): 15483-15494.
  6. Discovery of new covalent inhibitors of monoacylglycerol lipase with the nitrile warhead Via SCARdock.. Juanping Wang#, Xiaoyu Shi#, Junlai Wang, Qiang Zheng, Peipei Shao, Sen Liu*.
    • Bioorganic Chemistry, 2025, 159: 108378.
  7. Biological Significance and Therapeutic Promise of Programmed Ribosomal Frameshifting. Miora Bruna Marielle Ramamonjiharisoa#, Sen Liu*.
    • International Journal of Molecular Sciences, 2025, 26(3): 1294.
  8. Subtype-specific transcription factors affect polyamine metabolism and tumor microenvironment in breast cancer. Qi Song#, Yixuan Wang#, Sen Liu*.
    • Cancer Innovation, 2025, 4(1): e138.
  9. Structural insights into the mechanisms underlying polyaminopathies. Bing Wu#, Sen Liu*.
    • International Journal of Molecular Sciences, 2024, 25(12): 6340.
  10. Methods for inducing homologous protein dimerization. Junxia Guo#, Sen Liu*.
    • Progress in Biochemistry and Biophysics, 2024, 51(11):2805-2820.
  11. Effect of SUMOylation on maintaining mitochondrial dynamics balance by DRP1. Shuai Zhang#, Sen Liu*.
    • Progress in Biochemistry and Biophysics, 2024, 51(8): 1848-1859.
  12. An updated dataset and a structure-based prediction model for protein–RNA binding affinity. Xu Hong#, Xiaoxue Tong, Juan Xie, Pinyu Liu, Xudong Liu, Qi Song, Sen Liu, Shiyong Liu*.
    • Proteins: Structure, Function, Bioinformatics, 2023, 91(9): 1245-1253. 
  13. SCARdock: a web server and manually curated resource for discovering covalent ligands. Qi Song#, Lingyu Zeng#, Qiang Zheng, Sen Liu*. 
    • ACS Omega, 2023, 8(11): 10397–10402.
  14. Obtaining protein foldability information from models of AlphaFold2 and RoseTTAFold. Sen Liu#*, Kan Wu, Cheng Chen.
    • Computational and Structural Biotechnology Journal, 2022, 20: 4481-4489.
  15. RR3DD: an RNA global structure-based RNA three-dimensional structural classification database. Xu Hong#, Jinfang Zheng, Juan Xie, Xiaoxue Tong, Xudong Liu, Qi Song, Sen Liu, Shiyong Liu*.
    • RNA Biology, 2021, 18: 738-746. 
  16. Protein-DNA complex structure modeling based on structural template. Juan Xie#, Jinfang Zheng#, Xu Hong, Xiaoxue Tong, Xudong Liu, Qi Song, Sen Liu, Shiyong Liu*. 
    • Biochemical and Biophysical Research Communications, 2021, 577(5): 152-157.
  17. Dual inhibition of ornithine decarboxylase and A1 adenosine receptor efficiently suppresses breast tumor cells. Hongyan Ma#, Qizhang Li, Jing Wang, Jing Pan, Zhengding Su, Sen Liu*.
    • Frontiers in Oncology, 2021, 11: 636373.
  18. Discovery of covalent drugs targeting the key enzymes of SARS-CoV-2 using SCARdock. Qi Song#, Zhiying Wang#, Sen Liu*. In: Roy K. (eds) In Silico Modeling of Drugs Against Coronaviruses.
    • Methods in Pharmacology and Toxicology 2021: 291-306. Humana, New York, NY. 
  19. The optimization and applications of a cucurbit[6]uril-based real-time label-free method for evaluating the activity of ornithine decarboxylase. Jing Wang#, Xiangchen Liu, Hongyan Ma, Qiang Chen, Sen Liu*.
    • Chinese Journal of Biotechnology, 2021, 37(8): 2903-2914.
  20. Potential clinical drugs as covalent inhibitors of the priming proteases of the spike protein of SARS-CoV-2. Qizhang Li#, Zhiying Wang#, Qiang Zheng, Sen Liu*.
    • Computational and Structural Biotechnology Journal, 2020, 18: 2200-2208.
  21. The rational discovery of multipurpose inhibitors of the ornithine decarboxylase. Xiaoying Chai#, Jingqiong Zhan#, Jing Pan#, Mengxi He, Bo Li, Jing Wang, Hongyan Ma, Yanlin Wang, Sen Liu*.
    • The FASEB Journal, 2020, 34(9): 10907-10921.
  22. Potential covalent drugs targeting the main protease of the SARS-CoV-2 coronavirus. Sen Liu#*, Qiang Zheng, Zhiying Wang.
    • Bioinformatics, 2020, 36(11): 3295-3298.
  23. Repurposing clinical drugs as AdoMetDC inhibitors using the SCAR strategy.Yan Zhang#, Qiang Zheng#, Yin Zhou, Sen Liu*.
    • Frontiers in Pharmacology, 2020, 11: 248.
  24. Better together: Elements of successful scientific software development in a distributed collaborative community. Julia Koehler Leman#,*, Brian Weitzner#,*, Douglas Renfrew, Steven Lewis, Rocco Moretti, Andrew Watkins, Vikram Khipplel Mulligan, Sergey Lyskov, Jared Adolf-Bryfogle, Jason Labonte, Justyna Krys, RosettaCommons Consortium, Christopher Bystroff, William Schief, Dominik Gront, Ora Schueler-Furman, David Baker, Philip Bradley, Roland Dunbrack, Tanja Kortemme, Andrew Leaver-Fay, Charlie Strauss, Jens Meiler, Brian Kuhlman, Jeffrey Gray*, Richard Bonneau*.
    • PLOS Computational Biology, 2020,16(5): e1007507.
    • RosettaCommons Consortium Group author
  25. The recovery of KaiA’s activity depends on its N-terminal domain and KaiB in the cyanobacterial circadian clock. Jinkui Li#, Yongqi Huang, Zhengding Su, Sen Liu*.
    • Biochemical and Biophysical Research Communications, 2020, 524(1): 123-128.
  26. Electrostatic interactions in molecular recognition of intrinsically disordered proteins. Jing Yang#, Yifan Zeng, Yunfei Liu, Meng Gao, Sen Liu, Zhengding Su, Yongqi Huang*.
    • Journal of Biomolecular Structure and Dynamics, 2020, 38(16): 4883-4894.
  27. Polyamines disrupt the KaiABC oscillator by inducing protein denaturation. Jinkui Li#, Lingya Zhang, Junwen Xiong, Xiyao Cheng, Yongqi Huang, Zhengding Su, Ming Yi*, Sen Liu*.
    • Molecules, 2019, 24(18): 3351.
  28. Intrinsically Disordered Transactivation Domains Bind to TAZ1 Domain of CBP via Diverse Mechanisms. Meng Gao#, Jing Yang, Sen Liu, Zhengding Su, Yongqi Huang*.
    • Biophysical Journal, 2019, 117(7): 1301-1310.
  29. Structure-based reconstruction of a Mycobacterium hypothetical protein into an active Δ5–3-ketosteroid isomerase. Fei Peng#, XiyaoCheng, Hongwei Wang, Shikui Song, Tian Chen, Xin Li, Yijun He, Yongqi Huang, Sen Liu, Fei Yang*, Zhengding Su*.
    • BBA – Proteins and Proteomics, 2019, 1867(9): 821-830.
  30. Recombinant butelase-mediated cyclization of the p53-binding domain of the oncoprotein MdmX stabilized protein conformation as a promising model for structural investigation. Ni Pi#, Meng Gao, Xiyao Cheng, Huili Liu, Zhengkun Kuang, Zixin Yang, Jing Yang, Bailing Zhang, Yao Chen, Sen Liu, Yongqi Huang, Zhengding Su*.
    • Biochemistry, 2019, 58(27): 3005-3015.
  31. The influence of intrinsic folding mechanism of an unfolded protein on the coupled folding‐binding process during target recognition. Junwen Xiong#, Meng Gao#, Jingjing Zhou, Sen Liu, Zhengding Su*, Zhirong Liu, Yongqi Huang*.
    • Proteins: Structure, Function, Bioinformatics, 2019, 87(4): 265-275.
  32. The influence of KaiA mutations on its function in the KaiABC circadian clock system. Qiang Chen#, Sen Liu*, Liting Yang, Lingya Zhang, Jinkui Li.
    • Data in Brief, 2018, 18: 241-247.
  33. Kallikrein-related peptidase 7 is a potential target for the treatment of pancreatic cancer. Jianping Du#, Lin Li#, Jun Zheng*, Ding Zhang, Wei Liu, Weihong Zheng, Xiaosong Li, Rucheng Yao, Fangyu Wang, Sen Liu*, Xiao Tan*.
    • Oncotarget, 2018, 9: 12894-12906.
  34. The reversible function switching of the circadian clock protein KaiA is encoded in its structure. Qiang Chen#, Sen Liu*, Liting Yang, Lingya Zhang, Jinkui Li. 
    • Biochimica et Biophysica Acta (BBA)-General Subjects, 2017, 1861(11): 2535-2542.
  35. 3D-quantitative structure–activity relationship and docking studies of coumarin derivatives as tissue kallikrein 7 inhibitors. Xin Zheng#, Mengxi He#, Xiao Tan*, Jun Zheng, Fangyu Wang, Sen Liu*.
    • Journal of Pharmacy and Pharmacology, 2017, 69(9): 1136-1144.
  36. Expression and Purification of Cyanobacterial Circadian Clock Protein KaiC and Determination of Its Auto-phosphatase Activity. Qiang Chen#, Lingling Yu*, Xiao Tan*, Sen Liu*.
    • Bio-protocol, 2017, 7(04): e2140.
  37. Discovery of covalent ligands via noncovalent docking by dissecting covalent docking based on a “steric-clashes alleviating receptor (SCAR)” strategy. Yuanbao Ai#, Lingling Yu#, Xiao Tan#, Xiaoying Chai, Sen Liu*.
    • Journal of Chemical Information and Modeling, 2016, 56(8): 1563-1575.
    • Cover Article
  38. A dynamic interaction process between KaiA and KaiC is critical to the cyanobacterial circadian oscillator. Pei Dong#, Ying Fan, Jianqiang Sun, Mengting Lv, Ming Yi, Xiao Tan, Sen Liu*.  
    • Scientific Reports, 2016, 6: 25129.
  39. Two Sensitive Fluorescent BOPIM Probes with Tunable TICT Character for Low-Level Water Detection in Organic Solvents. Ping Shen#, Min Li, Chunlin Liu, Wei Yang, Sen Liu, Changying Yang*.
    • Journal of Fluorescence, 2016, 26(1): 363-369.
  40. Discovery of novel inhibitors of human S-adenosylmethionine decarboxylase based on in silico high-throughput screening and a non-radioactive enzymatic assay. Chenzeng Liao#, Yanlin Wang, Xiao Tan, Lidan Sun, Sen Liu*.
    • Scientific Reports, 2015, 5: 10754.
  41. Reliable cell cycle commitment in budding yeast is ensured by signal integration. Xili Liu#, Xin Wang#, Xiaojing Yang, Sen Liu, Lingli Jiang, Yimiao Qu, Lufeng Hu, Qi Ouyang, Chao Tang*.
    • eLife, 2015, 4: e03977.
  42. The Mechanism of KaiB-KaiC Interaction of the Cyanobacterial Circadian Oscillator. Song Liu#, Sen Liu*. 
    • Progress in Biochemistry and Biophysics, 2015, 42(3): 220-227.
  43. The P2/P2′ Sites Affect the Substrate Cleavage of TNF-alpha Converting Enzyme (TACE). Sen Liu#*, Song Liu, Yanlin Wang, Zhaojiang Liao. 
    • Molecular Immunology, 2014, 62(1): 122-128.
  44. Advances in the molecular mechanism of the core circadian oscillator of cyanobacteria. Weiqun Chen#, Song Liu, Sen Liu*. 
    • Acta Biophysica Sinica, 2013, 29(11): 801-810.
  45. Identification of a Possible Specific Non-continuous Epitope in Human P2X7 Receptor. Sen Liu#*, Chaoqi Liu. 
    • Asia Life Sciences, 2013, 22(1): 41-50.
  46. Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair. Gregory T. Kapp#, Sen Liu#, Derek T. Wong, Attila Reményi, Brian Yeh, Jack Taunton, Wendell A. Lim, and Tanja Kortemme*. 
    • Proc. Natl. Acad Sci USA, 2012, 109(14): 5277-5282.
    • “From the Cover” paper.
    • Commentary: PNAS April 3, 2012 vol. 109 no. 14: 5140-5141.
  47. Nonnatural protein–protein interaction-pair design by key residues grafting. Sen Liu#, Shiyong Liu#, Xiaolei Zhu, Huanhuan Liang, Aoneng Cao, Zhijie Chang, Luhua Lai*.
    • Proc. Natl. Acad Sci USA, 2007, 104(13) : 5330-5335.
  48. Expression, purification, crystallization and preliminary crystallographic study of a potential metal-dependent hydrolase with cyclase activity from Thermoanaerobacter tengcongensis. Sen Liu#, Guangteng Wu, Qichen Huang*, Luhua Lai,Youqi Tang, Hideaki Unnob, Masami Kusunoki.
    • Acta Crystallogr Sect F, 2005, 61(1): 90-92.

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