publications

2025

1. APSB

   PhenoModel: A multimodal phenotypic drug design foundation model for discovering novel potential inhibitors of multiple cancer cells

   Shihang Wang, Qilei Han, Weichen Qin, and 8 more authors

   Acta Pharmacologica Sinica B, 2025

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   PhenoModel is a cutting-edge molecular representation foundation model that integrates cell phenotype data to enhance the characterization of molecules. By leveraging the rich information embedded in cell images, PhenoModel significantly improves performance in various drug discovery tasks, particularly in virtual screening. Based on PhenoModel, we developed an active compound screening pipeline called PhenoScreen to further screen other molecules with similar activities but novel scaffolds according to the known active compounds.

   @article{wang2024phenomodel,
     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 Zhao, Yiqun and Ren, Pengxuan and Zhang, Yunze and Tang, Yilin and Li, Ruifeng and others},
     journal = {Acta Pharmacologica Sinica B},
     year = {2025},
     publisher = {Elsevier},
   }

2. APS

   Discovery of novel GluN1/GluN3A NMDA receptor inhibitors using a deep learning-based method

   Shi-hang Wang, Yue Zeng, Hao Yang, and 7 more authors

   Acta Pharmacologica Sinica, 2025

   DOI Bib

   @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},
     pages = {1--8},
     year = {2025},
     doi = {10.1038/s41401-025-01571-1},
     publisher = {Nature Publishing Group},
     url = {https://doi.org/10.1038/s41401-025-01571-1},
   }

3. JCIM

   DeepPSA: A Geometric Deep Learning Model for PROTAC Synthetic Accessibility Prediction

   Ran Zhang, Shihang Wang, Lin Wang, and 3 more authors

   Journal of Chemical Information and Modeling, 2025

   PMID: 40560790

   DOI
4. npjDD

   Recent advances in molecular representation methods and their applications in scaffold hopping

   Shihang Wang, Ran Zhang, Xiangcheng Li, and 1 more author

   npj drug discovery, 2025

   DOI Bib

   @article{doi:10.1038/s44386-025-00017-2,
     author = {Wang, Shihang and Zhang, Ran and Li, Xiangcheng and Bai, Fang},
     title = {Recent advances in molecular representation methods and their applications in scaffold hopping},
     journal = {npj drug discovery},
     volume = {2},
     number = {14},
     pages = {null},
     year = {2025},
     doi = {10.1038/s44386-025-00017-2},
     url = {https://doi.org/10.1038/s44386-025-00017-2},
     zhiyaobang = {https://mp.weixin.qq.com/s/bIB1Z496KNqdjDNcvP6FYw},
   }

2024

1. Adv Sci

   Conformational Space Profiling Enhances Generic Molecular Representation for AI-Powered Ligand-Based Drug Discovery

   Lin Wang, Shihang Wang, Hao Yang, and 6 more authors

   Advanced Science, 2024

   Bib

   @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},
     publisher = {Wiley Online Library},
   }

2023

1. Environ Res

   Metagenomics revealing molecular profiles of microbial community structure and metabolic capacity in Bamucuo lake, Tibet

   Cai Wei, Dan Sun, Wenliang Yuan, and 8 more authors

   Environmental Research, 2023

   HTML
2. Molecules

   DeepmRNALoc: a novel predictor of eukaryotic mRNA subcellular localization based on deep learning

   Shihang Wang, Zhehan Shen, Taigang Liu, and 3 more authors

   Molecules, 2023

   Bib HTML

   @article{wang2023deepmrnaloc,
     title = {DeepmRNALoc: a novel predictor of eukaryotic mRNA subcellular localization based on deep learning},
     author = {Wang, Shihang and Shen, Zhehan and Liu, Taigang and Long, Wei and Jiang, Linhua and Peng, Sihua},
     journal = {Molecules},
     volume = {28},
     number = {5},
     pages = {2284},
     year = {2023},
     publisher = {MDPI},
   }

3. J Cheminfo

   

   DeepSA: a deep-learning driven predictor of compound synthesis accessibility

   Shihang Wang, Lin Wang, Fenglei Li, and 1 more author

   Journal of Cheminformatics, 2023

   Abs DOI Bib HTML PDF

   

   DeepSA is proposed to predict synthesis accessibility of compounds, and has a much higher early enrichment rate in discriminating molecules that are difficult to synthesize. This helps users to select less expensive molecules for synthesis, thus reducing the time for drug discovery and development. You can use DeepSA on a webserver at https://bailab.siais.shanghaitech.edu.cn/deepsa

   @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},
     doi = {10.1186/s13321-023-00771-3},
     drugai = {https://mp.weixin.qq.com/s/LyvFQ74dHtEG1MO2j1LXbA},
     zhiyaobang = {https://mp.weixin.qq.com/s/WRVKF9LvC4t_ISyhrNbybQ},
   }

4. Molecules

   Computer-aided prediction of the interactions of viral proteases with antiviral drugs: antiviral potential of broad-spectrum drugs

   Pengxuan Ren, Shiwei Li, Shihang Wang, and 2 more authors

   Molecules, 2023

2022

1. JMV

   Molecular evolutionary characteristics of SARS-CoV-2 emerging in the United States

   Shihang Wang, Xuanyu Xu, Cai Wei, and 7 more authors

   Journal of medical virology, 2022

   DOI Bib HTML

   @article{wang2022molecular,
     title = {Molecular evolutionary characteristics of SARS-CoV-2 emerging in the United States},
     author = {Wang, Shihang and Xu, Xuanyu and Wei, Cai and Li, Sicong and Zhao, Jingying and Zheng, Yin and Liu, Xiaoyu and Zeng, Xiaomin and Yuan, Wenliang and Peng, Sihua},
     journal = {Journal of medical virology},
     volume = {94},
     number = {1},
     pages = {310--317},
     year = {2022},
     publisher = {Wiley Online Library},
     doi = {10.1002/jmv.27331},
   }

2. JBCB

   Clarifying real receptor binding site between coronavirus HCoV-HKU1 and 9-O-Ac-Sia based on molecular docking

   Xiaoyu Liu, Jingying Zhao, Sicong Li, and 8 more authors

   Journal of Bioinformatics and Computational Biology, 2022

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