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news_and_events [2019/07/18 13:21]
xfel
news_and_events [2020/04/03 08:09] (current)
xfel
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 ===== News ===== ===== News =====
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 +**Apr, 2020** The year of the Mouse (2020) started in a hard mode. The outbreak of COVID-19 (a pneumonia caused by the SARS-CoV-2 virus) evolved into a global crisis (WHO announced pandemic!). Since Jan 23rd, 2020, we have been working from home most of time. Nonetheless,​ we kept being productive, and continue contributing to the understanding of biological molecules. We have three papers published:
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 +(1) **Nepre**, Neighborhood Preference, the statistical analysis on protein structures, from which a new empirical potential energy is derived to assess predicted model qualities. The work is done mostly by intern students from USTC (school of software engineering),​ Siyuan Liu(刘思源),​ Xilun Xiang(向希伦),​ and Xiang Gao(高翔). It is published on **Scientific Reports** (https://​www.nature.com/​articles/​s41598-020-61205-w),​ and the source codes are available here: https://​github.com/​LiuLab-CSRC/​NePre .
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 +(2) **decodeSAXS**,​ using machine learning methods to build 3D models for 1D SAXS (small angle x-ray scattering) data. This is the first time that the auto-encoder approach applied in reverse modeling. It demonstrate that the 3D information can be compressed using auto-encoder neural networks and well represented using much smaller number of parameters. The work is published in **iScience** (a new journal by Cell publisher). https://​www.cell.com/​iscience/​fulltext/​S2589-0042(20)30090-0 by intern students, Hao He (何皓) and Can Liu (刘灿). The online webserver and program codes are available here:  http://​liulab.csrc.ac.cn/​decodeSAXS.
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 +(3) **SPIND-TC**,​ a crystallography analysis program that can index bragg peak signals of two-color diffraction patterns. This can be applied in serial crystallography that used multiple wavelengths for diffraction. Xuanxuan Li (李选选) and Chufeng Li (李楚峰) are the developers. The work is published on **Acta Crystallography A: foundations & Advances** (editor thinks it belongs to Foundations) http://​journals.iucr.org/​a/​issues/​2020/​03/​00/​ib5084/​index.html . The software is available at : https://​github.com/​lixx11/​SPIND-TC .
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 +There is another work that I contributed to long long time ago (2012 or 2013?). In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors. **Nat Commun** 11, 620 (2020). https://​doi.org/​10.1038/​s41467-020-14484-w by Nass, K., Redecke, L., Perbandt, M. et al. . Sometimes, it does take that long to get work done. m(
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 +We also participated in the fight against Covid-19, from two aspects:
 +(1) working at molecular level, trying to understand the binding of the virus spike protein to the human ACE2 receptor that facilitate the fusion of the virus. The work is shared online at https://​www.biorxiv.org/​content/​10.1101/​2020.03.24.005561v2 **Computational simulations reveal the binding dynamics between human ACE2 and the receptor binding domain of SARS-CoV-2 spike protein** ​
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 +(2) working at disease spreading model, trying to model and predict the disease progression and the impact of intervention to contain the spreading. https://​arxiv.org/​abs/​2003.07353,​ **Calibrated Intervention and Containment of the COVID-19 Pandemic**
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 **July, 2019** The special issue on XFEL crystallography and drug discovery is published in the International Journal of Molecular Sciences (https://​www.mdpi.com/​journal/​ijms/​special_issues/​XFEL). Prof. Lee and I wrote an editorial: The XFEL Protein Crystallography:​ Developments and Perspectives. Int. J. Mol. Sci. 2019, 20(14), 3421; https://​doi.org/​10.3390/​ijms20143421 **July, 2019** The special issue on XFEL crystallography and drug discovery is published in the International Journal of Molecular Sciences (https://​www.mdpi.com/​journal/​ijms/​special_issues/​XFEL). Prof. Lee and I wrote an editorial: The XFEL Protein Crystallography:​ Developments and Perspectives. Int. J. Mol. Sci. 2019, 20(14), 3421; https://​doi.org/​10.3390/​ijms20143421
  

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.