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:

(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 (, and the source codes are available here: .

(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). by intern students, Hao He (何皓) and Can Liu (刘灿). The online webserver and program codes are available here:

(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) . The software is available at : .

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). by Nass, K., Redecke, L., Perbandt, M. et al. . Sometimes, it does take that long to get work done. m(

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 Computational simulations reveal the binding dynamics between human ACE2 and the receptor binding domain of SARS-CoV-2 spike protein

(2) working at disease spreading model, trying to model and predict the disease progression and the impact of intervention to contain the spreading., Calibrated Intervention and Containment of the COVID-19 Pandemic

July, 2019 The special issue on XFEL crystallography and drug discovery is published in the International Journal of Molecular Sciences ( Prof. Lee and I wrote an editorial: The XFEL Protein Crystallography: Developments and Perspectives. Int. J. Mol. Sci. 2019, 20(14), 3421;

Jun, 2019 Congratulations to Xuanxuan Li. His software, ClickX, is published on the Journal of Applied Crystallography. This software is open source, fully based on Python, with excellent GUI support. It is designed for serial crystallography data screening, Details: Xuanxuan Li, Chufeng Li, Haiguang Liu*. ClickX: a visualization-based program for preprocessing of serial crystallography data. Journal of Applied Crystallography. 52, 674-682 (2019)

Jun, 2019 Congratulations to Lanqing Huang for the publication of his work on magnetic field induced dynamics of nanoparticles (collaboration with Prof. Can Xie in Peking University, Dr. Na Li in Protein Science Center in Shanghai). Details can be found here: Reversible rearrangement of magnetic nanoparticles in solution studied using time resolved SAXS method. Journal of Synchrotron Radiation, published online

May, 2019, Yufan Wang ( participated in the Shrec (shape retrieval contest) and the results have been published (see publication page).

Apr, 2019, the collaboration work with Prof. Weontae Lee's group is published in the International Journal of Molecular Sciences. Congratulations to Jaehyun Park and all authors. We helped with the data collection and analysis. It is the first structure determined at the Korean X-ray laser facility, PAL-XFEL: Non-Cryogenic Structure and Dynamics of HIV-1 Integrase Catalytic Core Domain by X-ray Free-Electron Lasers,

Mar, 2019 Computer aided protein engineering work on CXCR1 is published in Scientific Reports. This is a joint work with Prof. Weontae Lee's group from Yonsei University. Details can be found here:

Feb, 2019 The room temperature structure of light-driven chloride ion pumping rhodopsin is determined using the series femtosecond crystallography at LCLS (the XFEL facility located in the SLAC national laboratory). This is a joint work with Korean collaborators, Prof. Weontae Lee's group. Congratulations to Jihye and Xuanxuan. Details can be found here:

Feb, 2019 The single particle scattering analysis paper, coauthored by Yingchen Shi, Ke Yin, and many others is published on IUCrJ. Three classification methods were compared and data were analyzed for each subset of data. The most interesting observation is that the common dataset yielded the best resolution in the reconstructed 3D model. Check out more here: The source code used in this study can be found here: Congratulations to YingChen!

Jan, 2019 In collaboration with Arizona State University, we developed a new indexing algorithm and implemented in the SPIND using Python. The paper is published on IUCrJ: Congratulations to Xuanxuan and Chufeng! The source code is available at

Aug, 2018 We wrote a summary paper on XFEL and its applications in Structure Biology, published in 《物理》, to promote the education and research in X-ray Free Electron Lasers.

Aug, 2018 Our paper in collaboration with Prof. Z-J Liu from iHuman institute is published in Protein & Cell. It is about the disulfide bond engineering:

Mar 16, 2018 Our paper on “computational studies on CXCR1-IL8 complex structures” are published in Chinese Physics B, congratulations to Yang Wang and all. Here is the link to the paper:

Mar 16, 2018 Our paper on “ion distribution around amino acids in protein molecules” are published in BMC Bioinformatics, congratulations to Xilun Xiang. Here is the link to the paper:

Jan 27, 2018 The International workshop on image processing and inverse problems website is online for registration. Check out more here:

Oct 27, 2017 Our paper on merging heterogeneous core-shell nanoparticle scattering data is published in IUCrJ.

Oct 9, 2017 Welcome Siyuan Liu, from USTC, school of software engineering. He is an intern student, going to work with us for a year.

Sep 25, 2017 Congratulations to Xuanxuan Li, who is a contributing author of the Reflectin paper, published on Current Biology.

July 18, 2017 Welcome Dr. Cecylia Severin Lupala, originally from Tanzania, graduated from Barcelona Tech in Spain. She is a new postdoc.

July 6, 2017 Congratulations to Xuanxuan Li, who is a contributing author of the CB1 receptor with agonist, published in Nature.

July 3, 2017 Welcome Xiaoqun Dong & Can Liu, both from USTC, they will work here as intern students for a year.

June 30, 2017 Welcome Dr. Xubo Lin from Texas. He will work with us for a month.

June 23, 2017 The proceeding paper on protein shape retrieval is published. Congratulations to Na Song! Download PDF version.

June 2, 2017 Hongxiao defended his thesis, and he will pursue a Ph.D degree in Notre Dame University. Congratulations!

April 25, 2017 The paper on how to rank protein complex prediction structures using XFEL data is published. Congratulations to Hongxiao Wang. See here:

April 23-24, 2017 Na Song participated in EUROGRAPHICS Workshop on 3D Object Retrieval 2017, and gave a presentation on the track on bioshape retrievals.

April 11, 2017 The paper on nanoparticle single particle scattering XFEL data is online. Congratulations to Xuanxuan Li. See

Feb 25, 2017 Acceptance of the GPCR structure comparison paper, a new method for structural change description is developed. Congratulations to Dr. Ting Wang and Yang Wang. See

Feb 22, 2017 《物理》杂志发表 “冷冻电镜单颗粒技术的发展、现状与未来”的文章,祝贺黄岚青。“Application of cryo-electron microscopy in structure biology: current status and future perspectives”, See this:

Feb 20, 2017 Shrec 2017: special track on protein classification is finished.

Shrec 2017: special track on 3D shape classification of biological molecules

This track is organized by the group of computational structural biology ( in Beijing Computational Science Research Center (, as a section in the SHREC 2017, the 3D shape retrieval contest.


International Workshop On Image Processing and Inverse Problems

Date : Apr 21-24, 2018
Location : Beijing CSRC (计科中心)
Direction :
Subject :

The workshop is jointly organized by Institute of Applied Physics and Computational Mathematics and Beijing Computational Science Research Center. It aims to bring together experts on image processing and inverse problems based on optimization or PDEs. Topics of presentation are devoted to design and analysis of mathematical models, design and analysis of computational algorithms and applications of such models and algorithms to specific problems in industry.


Workshop on Imaging and Algorithm

Date : Dec 16-17, 2016
Location : Beijing CSRC (计科中心)
Direction :
Subject :
Multidisciplinary efforts in imaging and analysis, we hope to find a good way to apply mathematical models and algorithms to imaging technology, including image acquisition, storage, classification, merging, etc.
The goal of this workshop is to stimulate conversations between researchers using imaging techniques and the experts in mathematical modeling and algorithms.

Organizers: 台雪成刘海广 张智民,汲培文

Programs : Invited Speakers
Schedule : Meeting Schedule

Workshop on Protein Structure, Dynamics, and Functions

Date : Nov 24-25, 2016
Location : Beijing CSRC (计科中心), Conference room A203
Direction :

Subject : How to integrate computational methods with experimental data (especially those provides partial information) to better understand protein structure, dynamics and functions.
Programs : Details
Agenda : Schedule
print version
Organizing Committee : Haiguang Liu, Leihan Tang, Jooyoung Lee

more pictures

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.