研究领域
Innovative Drugs R&D
Our group aims to develop an interdisciplinary platform for innovative drugs research and design. The platform combines the world-leading computational biology technologies, ultra-large scale high-throughput virtual screening technologies and the AI algorithms based on our original molecular features. Our methods will streamline R&D efforts and proceed the drug discovery process.
Computational Biology
The dynamic characteristics including conformational and energetic information about biological macromolecular are deficient. Professor Arieh Warshel has established a theoretical system of computational biology and been awarded the 2013 Nobel Prize for Chemistry.
One of our goals is to understand the energy mechanisms of various macromolecular machines, especially drug targets, under the guidance of Warshel's theory. And then the molecular mechanisms and dynamic information would serve for drug design.
Currently, we focus on G protein-coupled receptor, SARS-CoV-2 spike, ATPases, ATP citrate lyase, etc.
AI Drug Design
Artificial intelligence (AI) has profoundly changed the mode of drug R&D. Compared with traditional methods, AI-aided drug design (AIDD) can explore much larger chemical space, thus improving the structural novelty of drug molecules.
Based on advanced AI drug design algorithms, such as GAN, VAE, and RNN etc., we creatively added kinetic properties of protein functional reactions to AI training.
The kinetic properties more accurately reflect the reality of a protein's functioning. Therefore, we can get the AI drug design model which has the best performance.
近期论文
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Multi-Responsive Peptide-Based Ultrathin Nanosheetsprepared By A Horizontal Monolayer Assembly Yanmei He, Xiaohong Zhu, Lei Wang, Yue Zhang, chen Bai, Dongdong wu Angewandte Chemie e202405765
Exploring The Activation Mechanism Of Metabotropic Glutamate 5 Receptor 2 Xiaohong Zhu, Mengqi Luo, Ke AN , Danfeng Shi, Tingjun Hou* , Arieh Warshel* , Chen Bai Proc. Natl. Acad. Sci. U.S.A. 121 (21) e2401079121
Guided Diffusion For Molecular Generation With Interaction Prompt Peng Wu, Huabin Du, Yingchao Yan, Tzong-Yi Lee, Chen Bai, Song Wu Briefings in Bioinformatics 2024, 25(3)
Mechanistic Study Of The Transmission Pattern Of The Sars-Cov-2 Omicron Variant Ke An, Xianzhi Yang, Mengqi Luo, Junfang Yan, Peiyi Xu, Honghui Zhang, Yuqing Li, Song Wu, Arieh Warshel, Chen Bai Proteins 2024; 1–15
Predicting Mutational Effects On Ca2+-Activated Chloride Conduction Of Tmem16a Based On A Simulation Study Yue Zhang, Kang Wu, Yuqing Li, Song Wu*, Arieh Warshel*, Chen Bai* J. Am. Chem. Soc. 2024, 146, 7, 4665–4679
Insights Into The Inhibitory Mechanisms Of The Covalent Drugs For Dnmt3a Wei Yang, Jingyuan Zhuang, Chen Li, Chen Bai, Guijuan Cheng I. J. Molecular Sciences 2023, 24(16), 12652
In Silico Optimization Of Sars-Cov-2 Spike Specific Nanobodies Xiaohong Zhu, Ke An, Junfang Yan, Peiyi Xu, Chen Bai Frontiers in Bioscience-Landmark 2023, 28(4), 67
Studies Of The Mechanism Of Nucleosome Dynamics: A Review On Multifactorial Regulation From Computational And Experimental Cases Danfeng Shi,Yuxin Huang, Chen Bai Polymers 2023, 15(7), 1763
Exploring The Phospholipid Transport Mechanism Of Atp8a1-Cdc50 Honghui Zhang, Yue Zhang, Peiyi Xu, Chen Bai Biomedicines 2023, 11(2), 546
A Systematic Study On The Binding Affinity Of Sars-Cov-2 Spike Protein To Antibodies Ke An, Xiaohong Zhu, Junfang Yan, Peiyi Xu, Linfeng Hu, Chen Bai AIMS Microbiology 2022, 8(4): 595-611
The Nature Of Functional Features Of Different Classes Of G-Protein-Coupled Receptors Ke An, Xiaohong Zhu, Chen Bai Biology 2022,11,1839
Application Of Computational Biology And Artificial Intelligence In Drug Design Yue Zhang, Mengqi Luo, Peng Wu, Song Wu, Tzong-Yi Lee, Chen Bai International Journal of Molecular Sciences 2022,23,13568
Mechanism Study Of Proteins Under Membrane Environment Yue Zhang, Xiaohong Zhu, Honghui Zhang, Junfang Yan, Peiyi Xu, Peng Wu, Song Wu, Chen Bai Membranes 2022, 12, 7, 694
Activation And Allosteric Regulation Of The Orphan Gpr88-Gi1 Signaling Complex Geng Chen, Jun Xu, Asuka Inoue, Maximilian F. Schmidt, Chen Bai, Qiuyuan Lu, Peter Gmeiner, Zheng Liu, Yang Du Nature Communications 2022, 13, 2375
Application Of Coarse-Grained (Cg) Models To Explore Conformational Pathway Of Large-Scale Protein Machines Danfeng Shi, Ke An, Honghui Zhang, Peiyi Xu, Chen Bai Entropy 2022, 24(5), 620
Mirtarbase Update 2022: An Informative Resource For Experimentally Validated Mirna–Target Interactions Hsi-Yuan Huang, Yang-Chi-Dung Lin, Shidong Cui, Yixian Huang, Yun Tang, Jiatong Xu, Jiayang Bao, Yulin Li, Jia Wen, Huali Zuo, Weijuan Wang, Jing Li, Jie Ni, Yini Ruan, Liping Li, Yidan Chen, Yueyang Xie, Zihao Zhu, Xiaoxuan Cai, Xinyi Chen, Lantian Yao, Yigang Chen, Yijun Luo, Shupeng LuXu, Mengqi Luo, Chih-Min Chiu, Kun Ma, Lizhe Zhu, Gui-Juan Cheng, Chen Bai, Ying-Chih Chiang, Liping Wang, Fengxiang Wei, Tzong-Yi Lee, Hsien-Da Huang Nucleic Acids Research 2022, 7;50(D1), D222-D230
Predicting Mutational Effects On Receptor Binding Of The Spike Protein Of Sars-Cov‑2 Variants Chen Bai, Junlin Wang, Geng Chen, Honghui Zhang, Ke An, Peiyi Xu, Yang Du, Richard D. Ye, Arjun Saha, Aoxuan Zhang, Arieh Warshel J. Am. Chem. Soc. 2021,143,42,17646-17654
Exploring The Activation Process Of The Β2ar‑Gs Complex Chen Bai, Junlin Wang, Dibyendu Mondal, Yang Du, Richard D. Ye, Arieh Warshel J. Am. Chem. Soc. 2021,143,29,11044-11051
The Catalytic Dwell In Atpases Is Not Crucial For Movement Against Applied Torque Chen Bai, Mojgan Asadi, Arieh Warshel Nature Chemistry 2020,12,12,1187-1192
Critical Differences Between The Binding Features Of The Spike Proteins Of Sars-Cov-2 And Sars-Cov Chen Bai, Arieh Warshel J. Phys. Chem. B 2020, 124, 28, 5907-5912
Revisiting The Protomotive Vectorial Motion Of F 0-Atpase Chen Bai, Arieh Warshel Proc. Natl. Acad. Sci. U.S.A. 2019, 116, 39, 19484-19489
On The Control Of The Proton Current In The Voltage-Gated Proton Channel Hv1 Myungjin Lee, Chen Bai, Mikolaj Feliks, Raphael Alhadeff, Arieh Warshel Proc. Natl. Acad. Sci. U.S.A. 2018, 115, 41, 10321-10326
Chemistry With Semi-Classical Electrons: Reaction Trajectories Auto-Generated By Sub-Atomistic Force Fields Chen Bai, Seyit Kale, Judith Herzfeld Chemical Science 2017,8,4203-4210
Special Pairs Are Decisive In The Autoionization And Recombination Of Water Chen Bai, Judith Herzfeld Journal of Physical Chemistry B 2017,121,16,4213-4219
Surface Propensities Of The Self-Ions Of Water Chen Bai, Judith Herzfeld ACS Central Science 2016,2,4,225-231
Molecular Dynamics Simulations Of Methanol-To-Olefin Reactions In Hzsm-5 Zeolite Using A Reaxff Force Field Chen Bai, Lianchi Liu, Huai Sun Journal of Physical Chemistry C 2012,116,12,7029-7039
Mechanism And Kinetics For The Initial Steps Of Pyrolysis And Combustion Of 1,6-Dicyclopropane-2,4-Hexyne From Reaxff Reactive Dynamics Lianchi Liu, Chen Bai, Huai Sun, William A. Goddard, III Journal of Physical Chemistry A 2011,115,19,4941-4950
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