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publications [2020/07/31 02:29]
xfel
publications [2021/09/07 09:59] (current)
xfel [2021]
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 ==Research articles== ==Research articles==
 +
 +====2021====
 +    -Liang Tian, Xuefei Li, Fei Qi,  Qian-Yuan Tang, Viola, ​ Tang, Jiang Liu,  Zhiyuan Li, Xingye Cheng, Xuanxuan Li,  Yingchen Shi,  **Haiguang Liu**, Lei-Han Tang*. Harnessing peak transmission around symptom onset for non-pharmaceutical intervention and containment of the COVID-19 pandemic, **Nature Communications**,​ 12, 1-12 (2021)
 +    - Vikash Kumar, **Haiguang Liu**, Chun Wu*, Drug repurposing against SARS-CoV-2 receptor binding domain using ensemble-based virtual screening and molecular dynamics simulations,​ **Computers in biology and medicine**, 135, 104634 (2021) ​  
 +    - Cecylia S. Lupala, Xuanxuan Li, Jian Lei, Hong Chen, Jianxun Qi, **Haiguang Liu***, Xiao-Dong Su*, Computational simulations reveal the binding dynamics between human ACE2 and the receptor binding domain of SARS-CoV-2 spike protein, **Quantitative Biology**, 2021, 9(1): 61-72. (Cover Article) https://​journal.hep.com.cn/​qb/​article/​2021/​2095-4689/​28794
 +    -Abdullahi Ibrahim Uba, Nicolas Scorese, Emily Dean, **Haiguang Liu***, and Chun Wu*, Activation Mechanism of Corticotrophin Releasing Factor Receptor Type 1 Elucidated Using Molecular Dynamics Simulations. **ACS Chem. Neurosci.** 2021 https://​pubs.acs.org/​doi/​abs/​10.1021/​acschemneuro.1c00126
 +    -Ji-Hye Yun#, Xuanxuan Li#, Jianing Yue, Jae-Hyun Park, Zeyu Jin, Chufeng Li, Hao Hu, Yingchen Shi, Suraj Pandey, Sergio Carbajo, Sébastien Boutet, Mark S. Hunter, Mengning Liang, Raymond G. Sierra, Thomas J. Lane, Liang Zhou, Uwe Weierstall, Nadia A. Zatsepin, Mio Ohki, Jeremy R. H. Tame, Sam-Yong Park, John C. H. Spence, Wenkai Zhang, Marius Schmidt*, Weontae Lee*, **Haiguang Liu***, Early-stage dynamics of chloride ion–pumping rhodopsin revealed by a femtosecond X-ray laser. **Proceedings of the National Academy of Sciences** Mar 2021, 118 (13) e2020486118;​ DOI: 10.1073/​pnas.2020486118 https://​www.pnas.org/​content/​118/​13/​e2020486118
 +    -Chun-Yan Liu, Lupala Cecylia Severin, Chang-Jiang Lyu, Wan-Li Zhu, Hong-Peng Wang, Cheng-Jun Jiang, Le-He Mei, **Hai-Guang Liu***, Jun Huang*, Improving thermostability of (R)-selective amine transaminase from Aspergillus terreus by evolutionary coupling saturation mutagenesis,​ **Biochemical Engineering Journal**, 167,107926 (2021) https://​doi.org/​10.1016/​j.bej.2021.107926.
  
 ====2020==== ====2020====
  
 +    -Ji-Hye Yun; Jae-Hyun Park; Zeyu Jin; Mio Ohki; Yang Wang; Cecylia Severin Lupala; Haiguang Liu; Sam-Yong Park; Weontae Lee. Structure-based functional modification study of a cyanobacterial chloride pump for transporting multiple anions. **Journal of Molecular Biology**. Published online on July 25th, 2020.
 +    - V Kumar, H Hoag, S Sader, N Scorese, H Liu, C Wu. GDP Release from the Open Conformation of Gα Requires Allosteric Signaling from the Agonist-Bound Human β2 Adrenergic Receptor. **Journal of Chemical Information and Modeling** 60 (8), 4064-4075
     - H. Wu, Y. Li, G. Liu, H. Liu* and N. Li*. SAS-cam: a program for automatic processing and analysis of small-angle scattering data, **J. Appl. Cryst.** (2020). 53 https://​doi.org/​10.1107/​S1600576720008985     - H. Wu, Y. Li, G. Liu, H. Liu* and N. Li*. SAS-cam: a program for automatic processing and analysis of small-angle scattering data, **J. Appl. Cryst.** (2020). 53 https://​doi.org/​10.1107/​S1600576720008985
-    - Y. Shi & H. Liu. EM-detwin: A Program for Resolving Indexing Ambiguity in Serial Crystallography Using the Expectation-Maximization Algorithm, **Crystals**,​ 2020, 10(7), 588; https://​doi.org/​10.3390/​cryst10070588 ​[[:​research:​ei5058_sascam.pdf|pdf]]+    - Y. Shi & H. Liu. EM-detwin: A Program for Resolving Indexing Ambiguity in Serial Crystallography Using the Expectation-Maximization Algorithm, **Crystals**,​ 2020, 10(7), 588; https://​doi.org/​10.3390/​cryst10070588 ​{{:​research:​ei5058_sascam.pdf|pdf}}
     - X. Gao, X. Dong, X. Li, Z. Liu, H. Liu, Prediction of disulfide bond engineering sites using a machine learning method, **Sci. Rep.** 10 (2020) 10330. https://​doi.org/​10.1038/​s41598-020-67230-z.     - X. Gao, X. Dong, X. Li, Z. Liu, H. Liu, Prediction of disulfide bond engineering sites using a machine learning method, **Sci. Rep.** 10 (2020) 10330. https://​doi.org/​10.1038/​s41598-020-67230-z.
     - P. Wang, L. Liu, A. Liu, L. Yan, Y. He, S. Shen, M. Hu, Y. Guo, H. Liu, C. Liu, Y. Lu, P. Wang, F. Deng, Z. Rao, Z. Lou, Structure of severe fever with thrombocytopenia syndrome virus L protein elucidates the mechanisms of viral transcription initiation, **Nat. Microbiol.** 5 (2020) 864–871. https://​doi.org/​10.1038/​s41564-020-0712-2. ​     - P. Wang, L. Liu, A. Liu, L. Yan, Y. He, S. Shen, M. Hu, Y. Guo, H. Liu, C. Liu, Y. Lu, P. Wang, F. Deng, Z. Rao, Z. Lou, Structure of severe fever with thrombocytopenia syndrome virus L protein elucidates the mechanisms of viral transcription initiation, **Nat. Microbiol.** 5 (2020) 864–871. https://​doi.org/​10.1038/​s41564-020-0712-2. ​
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   - Xuanxuan Li, John C. H. Spence, Brenda G. Hogue*, Haiguang Liu*. Merging single-shot XFEL diffraction data from inorganic nanoparticles:​ a new approach to size and orientation determination. **IUCrJ**, **4**, 741-750 (2017) http://​journals.iucr.org/​m/​issues/​2017/​06/​00/​it5013/​index.html ​   - Xuanxuan Li, John C. H. Spence, Brenda G. Hogue*, Haiguang Liu*. Merging single-shot XFEL diffraction data from inorganic nanoparticles:​ a new approach to size and orientation determination. **IUCrJ**, **4**, 741-750 (2017) http://​journals.iucr.org/​m/​issues/​2017/​06/​00/​it5013/​index.html ​
   - Zhe Guan, Tiantian Cai, Zhongmin Liu, Yunfeng Dou, Xuesong Hu, Peng Zhang, Xin Sun, Hongwei Li, Yao Kuang, Qiran Zhai, Hao Ruan, Xuanxuan Li, Zeyang Li, Qihui Zhu, Jingeng Mai, Qining Wang, Luhua Lai, Jianguo Ji, Haiguang Liu, Bin Xia, Taijiao Jiang, Shu-Jin Luo, Hong-Wei Wang, Can Xie. Origin of the Reflectin Gene and Hierarchical Assembly of Its Protein. **Current Biology**, **27**, 2833-2842. (2017) [[http://​www.sciencedirect.com/​science/​article/​pii/​S096098221730965X]]   - Zhe Guan, Tiantian Cai, Zhongmin Liu, Yunfeng Dou, Xuesong Hu, Peng Zhang, Xin Sun, Hongwei Li, Yao Kuang, Qiran Zhai, Hao Ruan, Xuanxuan Li, Zeyang Li, Qihui Zhu, Jingeng Mai, Qining Wang, Luhua Lai, Jianguo Ji, Haiguang Liu, Bin Xia, Taijiao Jiang, Shu-Jin Luo, Hong-Wei Wang, Can Xie. Origin of the Reflectin Gene and Hierarchical Assembly of Its Protein. **Current Biology**, **27**, 2833-2842. (2017) [[http://​www.sciencedirect.com/​science/​article/​pii/​S096098221730965X]]
-  - Hua T, Vemuri K, Nikas SP, Laprairie RB, Wu Y, Qu L, Pu M, Korde A, Jiang S, Ho JH, Han GW, Ding K, Li X, Liu H, Hanson MA, Zhao S, Bohn LM, Makriyannis A, Stevens RC, Liu ZJ. Crystal structures of agonist-bound human cannabinoid receptor CB1. **Nature** ​ **547**, 468–471 (2017) [[https://​www.nature.com/​nature/​journal/​v547/​n7664/​full/​nature23272.htm]]+  - Hua T, Vemuri K, Nikas SP, Laprairie RB, Wu Y, Qu L, Pu M, Korde A, Jiang S, Ho JH, Han GW, Ding K, Li X, Liu H, Hanson MA, Zhao S, Bohn LM, Makriyannis A, Stevens RC, Liu ZJ. Crystal structures of agonist-bound human cannabinoid receptor CB1. **Nature** ​ **547**, 468–471 (2017) [[https://​www.nature.com/​articles/​nature23272]]
   - Na Song, ..., Haiguang Liu*, SHREC'​17 Track: Protein Shape Retrieval, in Eurographics Workshop on 3D Object Retrieval, editor Ioannis Pratikakis, Florent Dupont, Maks Ovsjanikov. The Eurographics Association. (2017) http://​dx.doi.org/​10.2312/​3dor.20171055 Download {{ :​wiki:​shreck17:​csrc_protein_shrec.pdf | PDF}} version.   - Na Song, ..., Haiguang Liu*, SHREC'​17 Track: Protein Shape Retrieval, in Eurographics Workshop on 3D Object Retrieval, editor Ioannis Pratikakis, Florent Dupont, Maks Ovsjanikov. The Eurographics Association. (2017) http://​dx.doi.org/​10.2312/​3dor.20171055 Download {{ :​wiki:​shreck17:​csrc_protein_shrec.pdf | PDF}} version.
   - Hongxiao Wang, Haiguang Liu. Determining complex structures using docking method with single particle scattering data. **Front. Mol. Biosci**. **4**:23. http://​dx.doi.org/​10.3389/​fmolb.2017.00023 (2017)   - Hongxiao Wang, Haiguang Liu. Determining complex structures using docking method with single particle scattering data. **Front. Mol. Biosci**. **4**:23. http://​dx.doi.org/​10.3389/​fmolb.2017.00023 (2017)

Richard Feynman

“everything that is living can be understood in terms of the jiggling and wiggling of atoms”.

and now, we want to watch atoms jiggling and wiggling.

X-rays, electrons, fluorescence light, the advances of photon sciences, together with computational modeling, are making this happen.