@article{wang2020structural,
  title={The structural study of mutation-induced inactivation of human muscarinic receptor M4},
  author={Wang, Jingjing and Wu, Meng and Wu, Lijie and Xu, Yueming and Li, Fei and Wu, Yiran and Popov, Petr and Wang, Lin and Bai, Fang and Zhao, Suwen and others},
  journal={IUCrJ},
  volume={7},
  number={2},
  pages={294--305},
  year={2020},
  publisher={International Union of Crystallography}
}

@article{yang2020antimicrobial,
  title={Antimicrobial resistance in clinical Ureaplasma spp. and Mycoplasma hominis and structural mechanisms underlying quinolone resistance},
  author={Yang, Ting and Pan, Lianlian and Wu, Ningning and Wang, Lin and Liu, Zhen and Kong, Yingying and Ruan, Zhi and Xie, Xinyou and Zhang, Jun},
  journal={Antimicrobial Agents and Chemotherapy},
  volume={64},
  number={6},
  pages={10--1128},
  year={2020},
  publisher={American Society for Microbiology 1752 N St., NW, Washington, DC}
}

@article{wang2022discovery,
  title={Discovery of potential small molecular SARS-CoV-2 entry blockers targeting the spike protein},
  author={Wang, Lin and Wu, Yan and Yao, Sheng and Ge, Huan and Zhu, Ya and Chen, Kun and Chen, Wen-zhang and Zhang, Yi and Zhu, Wei and Wang, Hong-yang and others},
  journal={Acta Pharmacologica Sinica},
  volume={43},
  number={4},
  pages={788--796},
  year={2022},
  publisher={Springer Singapore Singapore}
}

@article{ren2022multi,
  title={A multi-targeting drug design strategy for identifying potent anti-SARS-CoV-2 inhibitors},
  author={Ren, Peng-xuan and Shang, Wei-juan and Yin, Wan-chao and Ge, Huan and Wang, Lin and Zhang, Xiang-lei and Li, Bing-qian and Li, Hong-lin and Xu, Ye-chun and Xu, Eric H and others},
  journal={Acta Pharmacologica Sinica},
  volume={43},
  number={2},
  pages={483--493},
  year={2022},
  publisher={Springer Singapore Singapore}
}

@article{li2021identification,
  title={Identification of potential binding sites of sialic acids on the RBD domain of SARS-CoV-2 spike protein},
  author={Li, Bingqian and Wang, Lin and Ge, Huan and Zhang, Xianglei and Ren, Penxuan and Guo, Yu and Chen, Wuyan and Li, Jie and Zhu, Wei and Chen, Wenzhang and others},
  journal={Frontiers in Chemistry},
  volume={9},
  pages={659764},
  year={2021},
  publisher={Frontiers Media SA}
}

@article{wang2021probing,
  title={Probing the allosteric inhibition mechanism of a spike protein using molecular dynamics simulations and active compound identifications},
  author={Wang, Qian and Wang, Lin and Zhang, Yumin and Zhang, XiangLei and Zhang, Leike and Shang, Weijuan and Bai, Fang},
  journal={Journal of Medicinal Chemistry},
  volume={65},
  number={4},
  pages={2827--2835},
  year={2021},
  publisher={American Chemical Society}
}

@article{wang2021ckb,
  title={CKB inhibits epithelial-mesenchymal transition and prostate cancer progression by sequestering and inhibiting AKT activation},
  author={Wang, Zheng and Hulsurkar, Mohit and Zhuo, Lijuan and Xu, Jinbang and Yang, Han and Naderinezhad, Samira and Wang, Lin and Zhang, Guoliang and Ai, Nanping and Li, Linna and others},
  journal={Neoplasia},
  volume={23},
  number={11},
  pages={1147--1165},
  year={2021},
  publisher={Elsevier}
}

@article{sun2022rapamycin,
  title={Rapamycin targets STAT3 and impacts c-Myc to suppress tumor growth},
  author={Sun, Le and Yan, Yu and Lv, Heng and Li, Jianlong and Wang, Zhiyuan and Wang, Kun and Wang, Lin and Li, Yunxia and Jiang, Hong and Zhang, Yaoyang},
  journal={Cell chemical biology},
  volume={29},
  number={3},
  pages={373--385},
  year={2022},
  publisher={Elsevier}
}

@article{hou2022target,
  title={Target-based virtual screening and LC/MS-guided isolation procedure for identifying phloroglucinol-terpenoid inhibitors of SARS-CoV-2},
  author={Hou, Bo and Zhang, Yu-Min and Liao, Han-Yi and Fu, Li-Feng and Li, De-Dong and Zhao, Xin and Qi, Jian-Xun and Yang, Wei and Xiao, Geng-Fu and Yang, Lian and others},
  journal={Journal of natural products},
  volume={85},
  number={2},
  pages={327--336},
  year={2022},
  publisher={American Chemical Society and American Society of Pharmacognosy}
}

@article{li2022recent,
  title={Recent advances in predicting protein--protein interactions with the aid of artificial intelligence algorithms},
  author={Li, Shiwei and Wu, Sanan and Wang, Lin and Li, Fenglei and Jiang, Hualiang and Bai, Fang},
  journal={Current Opinion in Structural Biology},
  volume={73},
  pages={102344},
  year={2022},
  publisher={Elsevier}
}

@article{wang2022crystal,
  title={Crystal structures of Wolbachia CidA and CidB reveal determinants of bacteria-induced cytoplasmic incompatibility and rescue},
  author={Wang, Haofeng and Xiao, Yunjie and Chen, Xia and Zhang, Mengwen and Sun, Guangxin and Wang, Feng and Wang, Lin and Zhang, Hanxiao and Zhang, Xiaoyu and Yang, Xin and others},
  journal={Nature Communications},
  volume={13},
  number={1},
  pages={1608},
  year={2022},
  publisher={Nature Publishing Group UK London}
}

@article{han2023discovery,
  title={Discovery, evaluation and mechanism study of WDR5-targeted small molecular inhibitors for neuroblastoma},
  author={Han, Qi-lei and Zhang, Xiang-lei and Ren, Peng-xuan and Mei, Liang-he and Lin, Wei-hong and Wang, Lin and Cao, Yu and Li, Kai and Bai, Fang},
  journal={Acta Pharmacologica Sinica},
  volume={44},
  number={4},
  pages={877--887},
  year={2023},
  publisher={Springer Nature Singapore Singapore}
}

@article{wang2022ppi,
  title={PPI-Miner: a structure and sequence motif co-driven protein--protein interaction mining and modeling computational method},
  author={Wang, Lin and Li, Feng-lei and Ma, Xin-yue and Cang, Yong and Bai, Fang},
  journal={Journal of Chemical Information and Modeling},
  volume={62},
  number={23},
  pages={6160--6171},
  year={2022},
  publisher={American Chemical Society}
}

@article{li2023synthesis,
  title={Synthesis of maleimide-braced peptide macrocycles and their potential anti-SARS-CoV-2 mechanisms},
  author={Li, Jian and Sun, Jina and Zhang, Xianglei and Zhang, Ruxue and Wang, Qian and Wang, Lin and Zhang, Leike and Xie, Xiong and Li, Chunpu and Zhou, Yu and others},
  journal={Chemical Communications},
  volume={59},
  number={7},
  pages={868--871},
  year={2023},
  publisher={The Royal Society of Chemistry}
}

@article{liu2022pilsl,
  title={PiLSL: pairwise interaction learning-based graph neural network for synthetic lethality prediction in human cancers},
  author={Liu, Xin and Yu, Jiale and Tao, Siyu and Yang, Beiyuan and Wang, Shike and Wang, Lin and Bai, Fang and Zheng, Jie},
  journal={Bioinformatics},
  volume={38},
  number={Supplement\_2},
  pages={ii106--ii112},
  year={2022},
  publisher={Oxford University Press}
}

@article{zhu2023propofol,
  title={Propofol exerts anti-anhedonia effects via inhibiting the dopamine transporter},
  author={Zhu, Xiao-Na and Li, Jie and Qiu, Gao-Lin and Wang, Lin and Lu, Chen and Guo, Yi-Ge and Yang, Ke-Xin and Cai, Fang and Xu, Tao and Yuan, Ti-Fei and others},
  journal={Neuron},
  volume={111},
  number={10},
  pages={1626--1636},
  year={2023},
  publisher={Elsevier}
}

@article{mei2023discovery,
  title={Discovery, structural optimization, and anti-tumor bioactivity evaluations of betulinic acid derivatives as a new type of ROR$\gamma$ antagonists},
  author={Mei, Lianghe and Xu, Lansong and Wu, Sanan and Wang, Yafang and Xu, Chao and Wang, Lin and Zhang, Xingyu and Yu, Chengcheng and Jiang, Hualiang and Zhang, Xianglei and others},
  journal={European Journal of Medicinal Chemistry},
  volume={257},
  pages={115472},
  year={2023},
  publisher={Elsevier Masson}
}

@article{jin2020structure,
  title={Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors},
  author={Jin, Zhenming and Du, Xiaoyu and Xu, Yechun and Deng, Yongqiang and Liu, Meiqin and Zhao, Yao and Zhang, Bing and Li, Xiaofeng and Zhang, Leike and Peng, Chao and others},
  journal={Nature},
  volume={582},
  number={7811},
  pages={289--293},
  year={2020},
  publisher={Nature Publishing Group UK London}
}

@article{wang2023deepsa,
  title={DeepSA: a deep-learning driven predictor of compound synthesis accessibility},
  author={Wang, Shihang and Wang, Lin and Li, Fenglei and Bai, Fang},
  journal={Journal of Cheminformatics},
  volume={15},
  number={1},
  pages={103},
  year={2023},
  publisher={Springer}
}

@article{liang2023new,
  title={A new variant of the colistin resistance gene MCR-1 with co-resistance to $\beta$-lactam antibiotics reveals a potential novel antimicrobial peptide},
  author={Liang, Lujie and Zhong, Lan-Lan and Wang, Lin and Zhou, Dianrong and Li, Yaxin and Li, Jiachen and Chen, Yong and Liang, Wanfei and Wei, Wenjing and Zhang, Chenchen and others},
  journal={PLoS Biology},
  volume={21},
  number={12},
  pages={e3002433},
  year={2023},
  publisher={Public Library of Science San Francisco, CA USA}
}

@article{fu2024salvianolic,
  title={Salvianolic acid B attenuates liver fibrosis by targeting Ecm1 and inhibiting hepatocyte ferroptosis},
  author={Fu, Yadong and Zhou, Xiaoxi and Wang, Lin and Fan, Weiguo and Gao, Siqi and Zhang, Danyan and Ling, Zhiyang and Zhang, Yaguang and Ma, Liyan and Bai, Fang and others},
  journal={Redox biology},
  volume={69},
  pages={103029},
  year={2024},
  publisher={Elsevier}
}

@article{wang2024conformational,
  title={Conformational space profiling enhances generic molecular representation for AI-powered ligand-based drug discovery},
  author={Wang, Lin and Wang, Shihang and Yang, Hao and Li, Shiwei and Wang, Xinyu and Zhou, Yongqi and Tian, Siyuan and Liu, Lu and Bai, Fang},
  journal={Advanced Science},
  volume={11},
  number={40},
  pages={2403998},
  year={2024}
}

@article{li2025nadph,
  title={NADPH-Independent Fluorescent Probe for Live-Cell Imaging of Heme Oxygenase-1},
  author={Li, Liang and Lu, Xuanyi and He, Qiyuan and Shu, Chao and Walter, Edward RH and Wang, Lin and Long, Nicholas J and Jiang, Lijun},
  journal={ACS sensors},
  volume={10},
  number={1},
  pages={499--506},
  year={2025},
  publisher={American Chemical Society}
}

@article{li2025mai,
  title={MAI-TargetFisher: A proteome-wide drug target prediction method synergetically enhanced by artificial intelligence and physical modeling},
  author={Li, Shi-wei and Ren, Peng-xuan and Wang, Lin and Han, Qi-lei and Li, Feng-lei and Li, Hong-lin and Bai, Fang},
  journal={Acta Pharmacologica Sinica},
  volume={46},
  number={5},
  pages={1462--1475},
  year={2025},
  publisher={Springer Nature Singapore Singapore}
}

@article{wang2025discovery,
  title={Discovery of novel GluN1/GluN3A NMDA receptor inhibitors using a deep learning-based method},
  author={Wang, Shi-hang and Zeng, Yue and Yang, Hao and Tian, Si-yuan and Zhou, Yong-qi and Wang, Lin and Chen, Xue-qin and Wang, Hai-ying and Gao, Zhao-bing and Bai, Fang},
  journal={Acta Pharmacologica Sinica},
  volume={46},
  number={11},
  pages={3108--3115},
  year={2025},
  publisher={Springer Nature Singapore Singapore}
}

@article{zhang2025deeppsa,
  title={DeepPSA: A Geometric Deep Learning Model for PROTAC Synthetic Accessibility Prediction},
  author={Zhang, Ran and Wang, Shihang and Wang, Lin and Tian, Siyuan and Tang, Yilin and Bai, Fang},
  journal={Journal of Chemical Information and Modeling},
  volume={65},
  number={13},
  pages={6861--6873},
  year={2025},
  publisher={American Chemical Society}
}

@article{wang2025recent,
  title={Recent advances in molecular representation methods and their applications in scaffold hopping},
  author={Wang, Shihang and Zhang, Ran and Li, Xiangcheng and Cai, Fengyu and Ma, Xinyue and Tang, Yilin and Xu, Chao and Wang, Lin and Ren, Pengxuan and Liu, Lu and others},
  journal={Npj Drug Discovery},
  volume={2},
  number={1},
  pages={14},
  year={2025},
  publisher={Nature Publishing Group UK London}
}

@article{wang2025phenomodel,
  title={PhenoModel: A multimodal phenotypic drug design foundation model for discovering novel potential inhibitors of multiple cancer cells},
  author={Wang, Shihang and Han, Qilei and Qin, Weichen and Wang, Lin and Yuan, Junhong and Cai, Fengyu and Zhao, Yiqun and Ren, Pengxuan and Zhang, Yunze and Tang, Yilin and others},
  journal={Acta Pharmaceutica Sinica B},
  year={2025},
  publisher={Elsevier}
}

@incollection{wang2026small,
  title={Small Molecule Conformation Prediction},
  author={Wang, Lin and Bai, Fang},
  booktitle={Artificial Intelligence for Drug Design},
  pages={527--546},
  year={2026},
  publisher={Springer}
}

@article{wang2026learned,
  title={Learned Conformational Space and Pharmacophore Into Molecular Foundational Model},
  author={Wang, Lin and Wu, Yifan and Luo, Hao and Liang, Minglong and Zhou, Yihang and Chen, Cheng and Liu, Chris and Zhang, Jun and Zhang, Yang},
  journal={Advanced Science},
  pages={e13556},
  year={2026}
}

@article{zhou2026proteinconformers,
  title={ProteinConformers: Benchmark Dataset for Simulating Protein Conformational Landscape Diversity and Plausibility},
  author={Zhou, Yihang and Wei, Chen and Sun, Minghao and Song, Jin and Li, Yang and Wang, Lin and Zhang, Yang},
  journal={Advances in Neural Information Processing Systems},
  volume={38},
  year={2026}
}

@article{lu2026molecular,
  title={Molecular glue degraders of HuR suppress BRAF-mutant colorectal cancer},
  author={Lu, Xiaocui and Wang, Xiuyun and Yang, Zheng and Wang, Xusheng and Wang, Lin and Xu, Chunhui and Lo, I and Geng, Chenlu and Pu, Yisheng and Zhang, Keyu and others},
  journal={Nature},
  pages={1--10},
  year={2026},
  publisher={Nature Publishing Group}
}

@article{liu2026integrating,
  title={Integrating chemical priors and physical laws to mitigate hallucinations in structure-based drug design},
  author={Liu, Zhongyu and Liu, Yadong and Zhou, Yihang and Liu, Zhiyuan and Yang, Yuhang and Wang, Zhiwen and Zang, Tianyi and Wang, Lin and Zhang, Yang},
  journal={Communications Chemistry},
  year={2026},
  publisher={Nature Publishing Group}
}