Publications

(Last Updated: Dec. 2025)

2025

He, W.$^{\dagger}$, Yang, C.$^{\dagger}$, Shi, X.$^{\dagger}$, Wang, Y.$^{\dagger}$, Wang, W., Schafer, A., Artman, B., Zhou, L., Liu, X., Tang, K. W. K., Jeong, J., He, Z., Garcia, H., Olivarez, A., Seeley, E. H., Yu, S., Romero-Lozano, A., Ren, P.$^*$, Bittner, G. D.$^*$, Wang, H.$^*$, A machine-learning-guided hydrogen-bonded organic framework for long-term, ultrasound-triggered pain therapy. bioRxiv, 2025. [bioRxiv]
Cui, G.$^{\dagger}$, Li, R.$^{\dagger}$, An, D.$^{\dagger}$, Xie, Y., Yu, C., Zou, W., Xia, Y., Zhang, Y., Feng, K., Xu, Z., Zheng, X., Jing, T., Yang, Y., Wang, Y., Wang, Z., Wang, L., Huang, J.$^*$, Zhang, Z.$^*$, Li, C.$^*$, Design and Synthesis of Novel Dual Inhibitors for JAK3 and TEC Kinases in Autoimmune Disorders. J. Med. Chem., 2025, 13, 13268-13294. [CrossRef]

2024

Jin, Z., Wang, Y. and Liu, C., Machine Learning Force Fields. In Springer Handbook of Chem- and Bioinformatics; Springer. (In Press) [Link]
Yang, Y.$^{\dagger}$, An, D.$^{\dagger}$, Wang, Y.$^{\dagger}$, Zou, W., Cui, G., Tong, J., Feng, K., Jing, T., Wang, L., Shi, L.$^*$ and Li, C.$^*$, Wee1 inhibitor optimization through deep-learning-driven decision making. Euro. J. Med. Chem., 2024, 280, 116912. [CrossRef]
Wang, Y., $^{\dagger}$, Jaffrelot Inizan T.$^{\dagger}$, Liu, C., Piquemal, J.-P.$^*$ and Ren, P.$^*$, Incorporating neural networks into the AMOEBA polarizable force field. J. Phys. Chem. B, 2024, 128, 2381-2388. [CrossRef] [ChemRxiv]

2023

Zhu, W., Wang, Y., Niu, Y., Zhang, L. and Liu, Z.$^*$, Current Trends and Challenges in Drug-Likeness Prediction: Are They Generalizable and Interpretable? Health Data Sci., 2023, 3, 98. [CrossRef]

2022

Wang, Y., Walker, B. D., Liu, C. and Ren, P.$^*$, An Efficient Approach to Large-Scale Ab Initio Conformational Energy Profiles of Small Molecules. Molecules, 2022, 27, 8567. [CrossRef]
Li, M.$^\dagger$, Hu, J.$^\dagger$, Wang, Y., Li, Y., Zhang, L.$^*$ and Liu, Z.$^*$, Challenging Reverse Screening: A Benchmark Study for Comprehensive Evaluation. Mol. Inform., 2022, 41, 2100063. [CrossRef]

2021

Lai, J.$^\dagger$, Li, X.$^\dagger$, Wang, Y., Yin, S., Zhou, J.$^*$ and Liu, Z.$^*$, AIScaffold: A Web-Based Tool for Scaffold Diversification Using Deep Learning. J. Chem. Inf. Model., 2021, 61, 1-6. [CrossRef]

2020

Lai, J.$^\dagger$, Hu, J.$^\dagger$, Wang, Y., Zhou, X., Li, Y., Zhang, L.$^*$ and Liu, Z.$^*$, Privileged Scaffold Analysis of Natural Products with Deep Learning‐based Indication Prediction Model. Mol. Inf., 2020, 39, 2000057. [CrossRef] [GitHub]
Wang, Y.$^\dagger$, Hu, J.$^\dagger$, Lai, J., Li, Y., Jin, H., Zhang, L., Zhang, L.$^*$ and Liu, Z.$^*$, TF3P: Three-dimensional Force Fields Fingerprint Learned by Deep Capsular Network. J. Chem. Inf. Model., 2020, 60, 2754-2765. [CrossRef] [arXiv.org] [GitHub]
Li, Y.$^\dagger$, Hu, J.$^\dagger$, Wang, Y., Zhou, J.$^*$, Zhang, L.$^*$, Liu, Z.$^*$, DeepScaffold: a comprehensive tool for scaffold-based de novo drug discovery using deep learning. J. Chem. Inf. Model., 2020, 60, 77-91. [CrossRef] [arXiv.org] [GitHub]

2019

Xia, X.$^\dagger$, Hu, J.$^\dagger$, Wang, Y., Zhang, L.$^*$ and Liu, Z.$^*$, Graph-based generative models for de novo drug design. Drug Discovery Today: Technol., 2019, 32, 45-53. [CrossRef]
Xue, Y.$^\dagger$, He, X.$^\dagger$, Yang, T., Wang, Y., Liu, Z., Zhang, G., Wang, Y., Wang, K.$^*$, Zhang, L.$^*$, Zhang, L., Discovery of fused heterocyclic carboxamide derivatives as novel $\alpha$7-nAChR agonists: Synthesis, preliminary SAR and biological evaluation. Euro. J. Med. Chem., 2019, 182, 111618. [CrossRef]
Dou, X., Huang, H., Li, Y., Jiang, L., Wang, Y., Jin, H., Jiao, N., Zhang, L., Zhang, L.$^*$, Liu, Z.$^*$, Multistage Screening Reveals 3-substituted Indolin-2-one Derivatives as Novel and Isoform Selective c-Jun N-terminal kinase 3 (JNK3) Inhibitors: Implications to Drug Discovery for Potential Treatment of Neurodegenerative Diseases. J. Med. Chem., 2019, 14, 6645-6664. [CrossRef]
Wang, Y.$^\dagger$, Dou, X.$^\dagger$, Jiang, L., Jin, H., Zhang, L., Zhang, L.$^*$ and Liu, Z.$^*$, Discovery of novel glycogen synthase kinase-3$\alpha$ inhibitors: Structure-based virtual screening, preliminary SAR and biological evaluation for treatment of acute myeloid leukemia. Euro. J. Med. Chem., 2019, 171, 221-234. [CrossRef]

2018

Hu, L.$^\dagger$, Liu, Y.$^\dagger$, Wang, Y., Wang, Z., Huang, J., Xue, Y., Liu, J., Liu, Z.$^*$, Chen, Y.$^*$ and Zhang, Y.$^*$, Discovery of acylphloroglucinol-based meroterpenoid enantiomers as KSHV inhibitors from Hypericum japonicum. RSC adv., 2018, 8, 24101-24109. [CrossRef]
Dou, X.$^\dagger$, Jiang, L.$^\dagger$, Wang, Y., Jin, H., Liu, Z.$^*$ and Zhang, L.$^*$, Discovery of new GSK-3$\beta$ inhibitors through structure-based virtual screening. Bioorg. Med. Chem. Lett, 2018, 28, 160-166. [CrossRef]