Research direction:
Artificial intelligence-based analytical methods, Cheminformatics and Bioinformatics
Contact information: 0086-28-85415695
Email: xmpuscu@scu.edu.cn
RESEARCH INTERESTS:
Combining experimental technique, machine learning and computer simulation to study:
1. Functional mechanisms of tumor-related genes and target proteins
2. Computer aided drug design
3. Artificial intelligence based material design
EDUCATION AND ACADEMIC CAREER:
1987~1991 BE in Analyze chemistry, Sichuan University of Science & Engneering
1995~1998 MSc in Analyze chemistry, Sichuan University
2000~2004 Ph.D. in Physical Chemistry, Sichuan University
2002~2003 Academic visitor, Department of Chemistry, Hong Kong Baptist University
1998~2010 Lecturer, Associated Professor, College of Chemistry, Sichuan University
2010~ current Professor, College of Chemistry, Sichuan University
SELECTED PUBLICATIONS:
1. Xin Chen, Kexin Wang, Jianfang Chen, Chao Wu, Jun Mao, Yuanpeng Song, Yijing Liu, Zhenhua Shao*, Xuemei Pu*, Integrative residue-intuitive machine learning and MD Approach to Unveil Allosteric Site and Mechanism for β2AR, Nature Communications, 2024, 15:8130
2. Jiali Guo, Songran Yang, Chenghui Wang, Jing Liu, Yanzhi Guo, Zongwei Yang, Xueyan Zhao, Xuemei Pu*, Cocrystal Prediction Tool (CCPT): A Web Server for Deep Learning Assisted Cocrystal Screening and Density Evaluation, Crystal Growth & Design, 2024, https://doi.org/10.1021/acs.cgd.4c00915
3. Ming Sun,‡ Caixia Fu,‡ Haoming Su, Ruyue Xiao, Chaojie Shi, Zhiyun Lu* and Xuemei Pu*，Enhancing chemistry-intuitive feature learning to improve prediction performance of optical properties, Chemical Science, 2024, DOI: 10.1039/d4sc02781g
4. Qiaolin Gou, Jing Liu, Haoming Su, Yanzhi Guo, Jiayi Chen, Xueyan Zhao, and Xuemei Pu*, Exploring an accurate machine learning model to quickly estimate stability of diverse energetic materials, iScience, 2024, 27:109452
5. Jianfang Chen, Yuanpeng Song, Luhan Ma, Yizhou Jin, Jin Yu, Yanzhi Guo, Yan Huang, Xuemei Pu,* Computational insights into diverse binding modes of the allosteric modulator and their regulation on dopamine D1 receptor, Computers in Biology and Medicine, 2024, 173: 108283
6. Jianfang Chen, Qiaoling Gou, Xin Chen, Yuanpeng Song, Fuhui Zhang*, Xuemei Pu*, Exploring biased activation characteristics by molecular dynamics simulation and machine learning for the l-opioid receptor, Physical Chemistry Chemical Physics, 2024, 26, 10698–10710
7. Shiqi Li, Xin Chen, Jianfang Chen, Binjian Wu, Jing Liu, Yanzhi Guo, Menglong Li *, Xuemei Pu*, Multi-omics integration analysis of GPCRs in pan-cancer to uncover inter-omics relationships and potential driver genes, Computers in Biology and Medicine, 2023, 161, 106988
8. Jing Hu, Songran Yang, Jun Mao, Chaojie Shi, Guangchuan Wang, Yijing Liu, and Xuemei Pu*, Exploring A General Convolutional Neural Network-Based Prediction Model For Critical Casting Diameter Of Metallic Glasses, Journal of Alloys and Compounds, 2023, 947, 169479.
9. Jiali Guo, Ming Sun, Xueyan Zhao, Chaojie Shi, Haoming Su, Yanzhi Guo, Xuemei Pu*, General Graph Neural Network-Based Model to Accurately Predict Cocrystal Density and Insight from Data Quality and Feature Representation, Journal of Chemical Information and Modeling, 2023, 63 (4), 1143–1156
10. Xin Chen, Yuan Yuan, Yichi Chen, Jin Yu, Jianfang Chen, Yanzhi Guo, Xuemei Pu,* Biased Activation Mechanism Induced by GPCR Heterodimerization: Observations from mu OR/delta OR Dimers, Journal of Chemical Information and Modeling, 2022, 62, 5581−5600
11. Shiqi Li, Jianfang Chen, Xin Chen, Jin Yu, Yanzhi Guo, Menglong Li* and Xuemei Pu*, Therapeutic and prognostic potential of GPCRs in prostate cancer from multi-omics landscape, Frontiers in Pharmacology, 2022, 13: 997664.
12. Chuan Li, Jiangting Liu, Jianfang Chen, Yuan Yuan, Jin Yu, Qiaolin Gou, Yan-Zhi Guo, Xuemei Pu*, An interpretable convolutional neural network Framework for Analyzing Molecular Dynamics Trajectories, a Case Study on Functional States for GPCRs, Journal of Chemical Information and Modeling, 2022, DOI: 10.1021/ acs.jcim.2c00085.
13. Fuhui Zhang, Yuan Yuan, Yichi Chen, Jianfang Chen, Yanzhi Guo, Xuemei Pu*, Molecular Insights into Allosteric Coupling Mechanism between Agonist and Two Different Transducers for μ-opioid receptor, Phys. Chem. Chem. Phys., 2022, 24, 5282-5293. (Elected Hot Article 2022).
14. Yuanyuan Jiang, Zongwei Yang, Jiali Guo, Hongzhen Li, Yijing Liu, Yanzhi Guo, Menglong Li, Xuemei Pu*, Coupling Complementary Strategy to Flexible Graph Neural Network for Quick Discovery of Coformer in Diverse Co-crystal Materials, Nature Communications, 2021, 12, 5950.
15. Jianfang Chen, Jiangting Liu, Yuan Yuan, Xin Chen, Fuhui Zhang, Xuemei Pu*, Molecular Mechanisms of Diverse Activation Stimulated by Different Biased Agonists for the β2-Adrenergic Receptor, Journal of Chemical Information and Modeling, 2021, DOI: 10.1021/acs.jcim.1c01016.
16. Fuhui Zhang, Xin Chen, Jianfang Chen, Yanjiani Xu, Shiqi Li, Yanzhi Guo, and Xuemei Pu*, Probing Allosteric Regulation Mechanism of W7.35 on Agonist Induced Activity for μOR by Mutation Simulation, Journal of Chemical Information and Modeling, 2021, DOI: 10.1021/acs.jcim.1c00650.
17. Yihuan Zhao, Caixia Fu, Ling Fu, Yijing Liu, Zhiyun Lu**, Xuemei Pu*, Data-driven machine learning models for quick prediction of thermal stability properties of OLED Materials, Materials Today Chemistry, 2021, 22, 100625.
18. Yunhao Xie, Yijing Liu, Renling Hu, Xu Lin, Jing Hu and Xuemei Pu *, A property-oriented adaptive design framework for rapid discovery of energetic molecules based on small-scale labeled datasets, RSC Advances, 2021, 11, 25764–25776.
19. Shiqi Li , Fuhui Zhang, Xiuchan Xiao, Yanzhi Guo, Zhining Wen, Menglong Li* and Xuemei Pu*，Prediction of Synergistic Drug Combinations for Prostate by Transcriptomic and Network Characteristics, Frontiers in Pharmacology, 2021, 12: 634097.
20. Ting Lei, Zhenxin Hu, Ruolin Ding, Jianfang Chen, Shiqi Li, Fuhui Zhang, Xuemei Pu,* and Nanrong Zhao*, Exploring the Activation Mechanism of a Metabotropic Glutamate 2 Receptor Homodimer via Molecular Dynamics Simulation, ACS Chemical Neuroscience, 2020, 11, 133-145.
21. Fuhui Zhang, Yuan Yuan, Minghui Xiang , Yanzhi Guo , Menglong Li ,Yijing Liu, Xuemei Pu*, Molecular Mechanism regarding Allosteric Modulation of Ligand Binding and the Impact of Mutations on Dimerization for CCR5 Homodimer. Journal of chemical information and modeling 2019. 59, 1965-1976.
22. Yu Liang, Li He, Yiru Zhao, Yingyi Hao, Yifan Zhou, Menglong Li, Chuan Li, Xuemei Pu*, Zhining Wen*, Comparative Analysis for the Performance of Variant Calling Pipelines on Detecting the de novo Mutations in Humans, Frontiers in Pharmacology, 2019, 10: 358.
23. Liting Shen, Yuan Yuan, Yanzhi Guo, Menglong Li, Chuan Li, Xuemei Pu*, Probing the Druggablility on the Interface of the Protein-protein Interaction and its Allosteric Regulation Mechanism on the Drug Screening for the CXCR4 Homodimer, Frontiers in Pharmacology, 2019, 10: 1310.
24. Longrong Wang, Yuan Yuan, Xin Chen, Jiangfan Chen, Yanzhi Guo, Menglong Li, Chuan Li and Xuemei Pu*, Probing the cooperative mechanism of the μ-δ opioid receptor heterodimer by multiscale simulation, Physical Chemistry Chemical Physics, 2018, 20, 29969—29982.
25. Liyun Zhang, Yuan Yuan , Tian Ren, Yanzhi Guo, Chuan Li*, Xuemei Pu*, Shining Light on Molecular Mechanism for Odor-selectivity of CNT-immobilized Olfactory Receptor. Scientific Reports 2018, 8:7824.
26. Xi Zhang, Yuan Yuan, Longrong Wang, Yanzhi Guo, Menglong Li, Chuan Li*, Xuemei Pu*: Use multiscale simulation to explore the effects of the homodimerizations between different conformation states on the activation and allosteric pathway for the μ-opioid receptor. Physical Chemistry Chemical Physics, 2018, 19：13485-13496.
27. Yihuan Zhao, YuanYuan, Jianfang Chen, MenglongLi, Xuemei Pu,* Chemometrics-enhanced high performance liquid chromatography strategy for simultaneous determination on seven nitroaromatic compounds in environmental water, Chemometrics and Intelligent Laboratory Systems, 2018, 174, 149-155.
28. Tao Liang, Yuan Yuan, Ran Wang, Yanzhi Guo, Menglong Li, Xuemei Pu,* and Chuan Li*, Structural Features and Ligand Selectivity for 10 Intermediates in the 2 Activation Process of β2-Adrenergic Receptor，ACS OMEGA，2017, 2, 8557 – 8567.
29. Suqing Li, Bin Li, Yuanting Zheng, Menglong Li, Leming Shi* and Xuemei Pu*, Exploring functions of long noncoding RNAs across multiple cancers through co-expression network, Scientific Reports, 2017, 7:754.
30. Liyun Zhang, Yuzhi Li, YuanYuan, Yuanyuan Jiang, Yanzhi Guo, Menglong Li, Xuemei Pu*, Molecular mechanism of carbon nanotube to activate Subtilisin Carlsberg in polar and non-polar organic media, Scientific Reports, 2016, 6:36838.
31. Nan Gao, Tao Liang, Yuan Yuan, Xiuchan Xiao, Yihuan Zhao, Yanzhi Guo, Menglong Li, Xuemei Pu*, Exploring mechanism of F282L mutation-caused constitutive activity of GPCR by a computational study, Physical Chemistry Chemical Physics, 2016, 18, 29412 – 29422.
32. Xiaojun Zeng, Liyun Zhang, Xiuchan Xiao , Yuanyuan Jiang , Yanzhi Guo, Xinyan Yu, Xuemei Pu*, Menglong Li*, Unfolding mechanism of thrombin-binding aptamer revealed by molecular dynamics simulation and Markov State Model. Scientific Reports, 2016, 6, 24065.
33. Jing Yi, Ying Xiong, Kemei Cheng, Menglong Li, Genbai Chu, Xuemei Pu*, Tao Xu*, A Combination of Chemometrics and Quantum Mechanics Methods Applied to Analysis of Femtosecond Transient Absorption Spectrum of Ortho-Nitroaniline, Scientific Reports, 2016, 6:19364.
34. Yan Jiao, Ming Li, Ning Wang, Tao Lu, Liang Zhou, Yan Huang, Zhiyun Lu,* Daibing Luo, and Xuemei Pu*, A facile color-tuning strategy for constructing a library of Ir(III) complexes with fine-tuned phosphorescence from bluish green to red using synergetic substituent effect of –OCH3 and –CN at merely the C-ring of C^N ligand, Journal of Material Chemistry C, 2016, 4, 4269-4277.
35. Minqi Wang, Xuan He, Qin Xiong, Runyu Jing, Yuxiang Zhang, Zhining Wen, Qifan Kuang, Xuemei Pu*, Menglong Li and Tao Xu, A facile strategy applied to simultaneous qualitative-detection on multiple components of mixture samples: a joint study of infrared spectroscopy and multi-label algorithms on PBX explosives, RSC Advances, 2016, 6, 4713–4722.
36. Tao Lu, Yuan Yuan, Yan Jiao, Zhining Wen, Lu Wang, Yihuan Zhao, Yuxiang Zhang, Menglong Li, Xuemei Pu*, Tao Xu*, Simultaneous spectrophotometric quantification of dinitrobenzene isomers in water samples using multivariate calibration methods, Chemometrics and Intelligent Laboratory Systems, 2016, 154, 72-79.
37. Liyun Zhang, Xiuchan Xiao, Yuan Yuan, Yanzhi Guo, Menglong Li, Xuemei Pu,* Probing Immobilization Mechanism of alpha-chymotrypsin onto Carbon Nanotube in Organic Media by Molecular Dynamics Simulation, Scientific Reports, 2015, 5: 9297.
38. Xiuchan Xiao, Xiaojun Zeng, Yuan Yuan, Nan Gao, Yanzhi Guo, Xuemei Pu*, Menglong Li*, Understanding the conformation transition in the activation pathway of β2 adrenergic Receptor via Target Molecular Dynamics Simulation. Physical Chemistry Chemical Physics, 2015, 17, 2512 – 2522
39. Yunqing Chen, Yi Wang, Yuan Yuan, Yan Jiao, Xuemei Pu,* and Zhiyun Lu*, Deactivation Mechanism of a Novel AIE-active Naphthalimide Derivative in More Polar Solutions. Physical Chemistry Chemical Physics, 2015, 17, 1309 – 1316.
40. Tao Lu, Yuan Yuan, Xuan He, Menglong Li, Xuemei Pu*, Tao Xu*, Zhining Wen, Simultaneous determination of multicomponent in explosives using ultraviolet spectrophotometry and partial least square method, RSC advances, 2015, 5, 13021 -13027.
41. Tao Lu, Zhining Wen, Lu Wang, Xuan He, Yuan Yuan, MinqiWang, Yihuan Zhao, Menglong Li, Xuemei Pu*, Tao Xu*, Quantitative determination on binary-component polymer bonded explosives: A joint study of ultraviolet spectrophotometry and multivariate calibration methods, Chemometrics and Intelligent Laboratory Systems, 2015, 147, 131–138.
