CompBio

1. CS Lupala, Y Ye, H Chen, XD Su, H Liu. Mutations on RBD of SARS-CoV-2 Omicron variant result in stronger binding to human ACE2 receptor. Biochemical and biophysical research communications 590, 34-41 (2022)

1. CS Lupala, V Kumar, X Su, C Wu, H Liu. Computational insights into differential interaction of mammalian angiotensin-converting enzyme 2 with the SARS-CoV-2 spike receptor binding domain. Computers in biology and medicine, 105017 (2021)
2. 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)
3. 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)
4. 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
5. 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
6. 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
7. 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.

1. 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.
2. 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
3. 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
4. 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 pdf
5. 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.
6. 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.
7. X. Li, C. Li, H. Liu, SPIND-TC: An indexing method for two-color X-ray diffraction data, Acta Crystallogr. Sect. A Found. Adv. 76 (2020) 369–375. https://doi.org/10.1107/S2053273320001916.
8. A.I. Uba, C. Radicella, C. Readmond, N. Scorese, S. Liao, H. Liu*, C. Wu*, Binding of agonist WAY-267,464 and antagonist WAY-methylated to oxytocin receptor probed by all-atom molecular dynamics simulations, Life Sci. 252 (2020) 117643. https://doi.org/10.1016/j.lfs.2020.117643.
9. Siyuan Liu, Xilun Xiang, Xiang Gao & Haiguang Liu*, Neighborhood Preference of Amino Acids in Protein Structures and its Applications in Protein Structure Assessment, Scientific Reports volume 10, Article number: 4371 (2020) https://www.nature.com/articles/s41598-020-61205-w
10. Hao He; Can Liu; Haiguang Liu* Model Reconstruction from Small-Angle X-Ray Scattering Data Using Deep Learning Methods. iScience 23(3) 100906 (2020). https://doi.org/10.1016/j.isci.2020.100906
11. Nass, K., Redecke, L., Perbandt, M. et al. 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

1. Y. Xu, Y. Wang, Y. Wang, K. Liu, Y. Peng, D. Yao, H. Tao, H. Liu and G. Song. Mutagenesis facilitated crystallization of GLP-1R. IUCrJ 6, 996-1006 (2019) https://journals.iucr.org/m/issues/2019/06/00/tj5027/index.html
2. Haiguang Liu*, Weontae Lee*: The XFEL Protein Crystallography: Developments and Perspectives. Int. J. Mol. Sci. 2019, 20(14), 3421; https://doi.org/10.3390/ijms20143421
3. 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) http://scripts.iucr.org/cgi-bin/paper?S1600576719005363
4. Huang Lanqing, Jingeng Mai, Qihui Zhu, Zhen Guo, Siying Qin, Peilin Yang, Xuanxuan Li, Yingchen Shi, Xiaotian Wang, Qining Wang, Na Li, Can Xie* & Haiguang Liu*. Reversible rearrangement of magnetic nanoparticles in solution studied using time resolved SAXS method. Journal of Synchrotron Radiation, (2019). 26, 1294-1301 https://journals.iucr.org/s/issues/2019/04/00/co5123/index.html
5. Langenfeld, Florent and Axenopoulos, Apostolos and Benhabiles, Halim and Daras, Petros and Giachetti, Andrea and Han, Xusi and Hammoudi, Karim and Kihara, Daisuke and Lai, Tuan M. and Liu, Haiguang and Melkemi, Mahmoud and Mylonas, Stelios K. and Terashi, Genki and Wang, Yufan and Windal, Feryal and Montes, Matthieu, Protein Shape Retrieval Contest, Eurographics Workshop on 3D Object Retrieval, https://doi.org/10.2312/3dor.20191058 (2019)
6. Jae-Hyun Park, Ji-Hye Yun, Yingchen Shi, Jeongmin Han, Xuanxuan Li, Zeyu Jin, Taehee Kim, Jaehyun Park, Sehan Park, Haiguang Liu* and Weontae Lee*, Non-Cryogenic Structure and Dynamics of HIV-1 Integrase Catalytic Core Domain by X-ray Free-Electron Lasers, Int. J. Mol. Sci. 2019, 20(8), 1943; https://doi.org/10.3390/ijms20081943
7. Yang Wang, Jae-Hyun Park, Cecylia Severin Lupala, Ji-Hye Yun, Zeyu Jin, Lanqing Huang, Xuanxuan Li, Leihan Tang, Weontae Lee & Haiguang Liu Computer aided protein engineering to enhance the thermo-stability of CXCR1- T4 lysozyme complex, Scientific Reports volume 9, Article number: 5317 (2019)https://www.nature.com/articles/s41598-019-41838-2
8. Yingchen Shi, Ke Yin, Xuecheng Tai, Hasan DeMirci, Ahmad Hosseinizadeh, Brenda G Hogue, Haoyuan Li, Abbas Ourmazd, Peter Schwander, Ivan A Vartanyants, Chun Hong Yoon, Andrew Aquila*, Haiguang Liu*，Evaluation of the performance of classification algorithms for XFEL single-particle imaging data. IUCrJ, 6(2), 331-340 (2019). http://journals.iucr.org/m/issues/2019/02/00/cw5020/index.html
9. Ji-Hye Yun#, Xuanxuan Li#, Jae-Hyun Park, Yang Wang, Mio Ohki, Zeyu Jin, Wonbin Lee, Sam-Yong Park, Hao Hu, Chufeng Li, Nadia Zatsepin, Mark S. Hunter, Raymond G. Sierra, Jake Koralek, Chun Hong Yoon, Hyun-Soo Cho, Uwe Weierstall, Leihan Tang, Haiguang Liu* and Weontae Lee*, Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency, Journal of Biological Chemistry 294, 794-804 (2019) http://www.jbc.org/content/294/3/794
10. Chufeng Li, Xuanxuan Li, Richard Kirian, John C. H. Spence, Haiguang Liu and Nadia A. Zatsepin*, SPIND: a reference-based auto-indexing algorithm for sparse serial crystallography data, IUCrJ, 6(1), 72-84 (2019) http://journals.iucr.org/m/issues/2019/01/00/cw5018/index.html

1. Wang, Yang, Cecylia S. Lupala, Haiguang Liu*, and Xubo Lin*. Current topics in medicinal chemistry 18, no. 27 : 2268-2277 (2018) https://doi.org/10.2174/1568026619666181212102856
2. Mengchen Pu, Zhijie Xu, Yao Peng, Yaguang Hou, Dongsheng Liu, Yang Wang, Haiguang Liu*, Gaojie Song*, Zhi-Jie Liu*, Protein Cell, 9(7): 659-663 (2018) https://link.springer.com/article/10.1007/s13238-017-0482-7
3. Wang T., H. Liu, Y. Duan. Assessment of the transmembrane domain structures in GPCR Dock 2013 models. J. of Structural Biology, 201 (3), 210-220 (2018) https://www.sciencedirect.com/science/article/pii/S1047847717301971
4. Shi Y. H. Liu. The principle of X-ray free electron lasers and their applications in biological molecular structure determination, Wuli 《物理》, 47, 426-436 (2018) http://www.wuli.ac.cn/CN/10.7693/wl20180703
5. Xilun Xiang, Haiguang Liu*, IDPM: an online database for ion distribution in protein molecules, BMC Bioinformatics, 19:102 (2018) https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2110-9
6. Yang Wang(王洋), Cecylia Severin Lupala, Ting Wang(王亭), Xuanxuan Li(李选选), Ji-Hye Yun, Jae-hyun Park, Zeyu Jin(金泽宇), Weontae Lee, Leihan Tan(汤雷翰), Haiguang Liu(刘海广), Chinese Physics B, 27(3), 038702 (2018) http://cpb.iphy.ac.cn/EN/abstract/abstract71722.shtml

1. 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
2. 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
3. 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
4. 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 PDF version.
5. 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)
6. Xuanxuan Li,…Haiguang Liu*, Diffraction data of coreshell nanoparticles from an X-ray free electron laser, Scientific Data, 4:170048. (2017) http://dx.doi.org/10.1038/sdata.2017.48
7. Ting Wang*, Yang Wang, Leihan Tang, Yong Duan*, Haiguang Liu*, 7×7 RMSD matrix: A new method for quantitative comparison of the transmembrane domain structures in the G-protein coupled receptors. J. of Structural Biology (2017) http://dx.doi.org/10.1016/j.jsb.2017.02.005 Download PDF version.
8. 黄岚青, 刘海广* “冷冻电镜单颗粒技术的发展、现状与未来”（ “Application of cryo-electron microscopy in structure biology: current status and future perspectives”），《物理》46 (2), 91-99, (2017) http://doi.org/10.7693/wl20170204 PDF

1. Coherent diffraction of single Rice Dwarf Virus particles using hard X-rays at the Linac Coherent Light Source. Munke A. et al., Scientific Data 3, 160064, doi:10.1038/sdata.2016.64 (2016)
2. XFEL data analysis for structural biology. Liu H. & J.C.H. Spence, Quantitative Biology 4: 159. doi:10.1007/s40484-016-0076-z (2016)
3. Facilitating model reconstruction for single-particle scattering using small-angle X-ray scattering methods. Ma, S. & Liu, H. J. Appl. Cryst. 49, 665-671 (2016)

1. Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser. Y. Kang et al., Nature 523 561–567 (2015)
2. Lipidic cubic phase serial millisecond crystallography using synchrotron radiation. P. Nogly et al., IUCrJ 2 168 (2015)
3. Serial femtosecond X-ray diffraction of enveloped virus microcrystals. R. M. Lawrence et al., Structural Dynamics 2 041720 (2015)
4. Solving protein nanocrystals by cryo-EM diffraction: Multiple scattering artifacts. G. Subramanian et al., Ultramicroscopy 148 87–93 (2015)

1. Ab-initio phasing using nanocrystal shape transforms with incomplete unit cells. H. Liu and N. A. Zatsepin and J. C. Spence IUCrJ 1 19–27 (2014)
2. Expression, purification and crystallization of CTB-MPR, a candidate mucosal vaccine component against HIV-1. H.-H. Lee et al., IUCrJ 1 305–317 (2014)
3. Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography. U. Weierstall et al., Nature communications 5 (2014)
4. Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser. C. Kupitz and S. Basu et al., Nature (2014) 513, 261
5. The indexing ambiguity in serial femtosecond crystallography (SFX) resolved using an expectation maximization algorithm. H. Liu and J. C. Spence IUCrJ 1 393–401 (2014)

1. Three-dimensional single-particle imaging using angular correlations from X-ray laser data. H. Liu and B. K. Poon and D. K. Saldin and J. C. Spence and P. H. Zwart Acta Crystallographica Section A: Foundations of Crystallography 69 365–373 (2013)
2. Computation of fluctuation scattering profiles via three-dimensional Zernike polynomials. H. Liu and B. K. Poon and A. J. Janssen and P. H. Zwart Acta Crystallographica Section A: Foundations of Crystallography 68 561–567 (2012)
3. Computation of small-angle scattering profiles with three-dimensional Zernike polynomials. H. Liu and R. J. Morris and A. Hexemer and S. Grandison and P. H. Zwart Acta Crystallographica Section A: Foundations of Crystallography 68 278–285 (2012)
4. Determining pair distance distribution function from SAXS data using parametric functionals. H. Liu and P. H. Zwart Journal of structural biology 180 226–234 (2012)
5. The Small Angle Scattering ToolBox (SASTBX): an open-source software for biomolecular small-angle scattering. H. Liu and A. Hexemer and P. Zwart Journal of Applied Crystallography 45 587–593 (2012)
6. Effects of posttranslational modifications on the structure and dynamics of histone H3 N-terminal peptide. H. Liu and Y. Duan Biophysical journal 94 4579–4585 (2008)
7. Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations. H. Lei and C. Wu and H. Liu and Y. Duan Proceedings of the National Academy of Sciences 104 4925 (2007)
8. Designability and cooperative folding in a fourletter hydrophobic-polar model of proteins H. Liu and LH Tang Physical Review E 74 051918 (2006)

The dynamics of nucleosome systems and the posttranslational modification effects: Applications of molecular dynamics simulation in structural biology H. Liu (2009)

Conformational Changes in Protein Function. H. Liu and S. G. Dastidar and H. Lei and W. Zhang and M. C. Lee and Y. Duan METHODS IN MOLECULAR BIOLOGY 443 259 (2008)