Publications

Zhu, H., Yuan, S., Tang, M. et al.. Molecular graph-based invariant representation learning with environmental inference and subgraph generation for out-of-distribution generalization. Journal of Cheminformatics. (2026) DOI: 10.1186/s13321-025-01142-w

molecular representation medical chemistry

Xu, K., Wang, J., Liu, M., Zhou, K., Lin, S., Li, W., Shi, L., Zhou, P., Liu, H. and Yao, X.. Efficient Generation of Protein and Protein-Protein Complex Dynamics via SE(3)-Parameterized Diffusion Models. Journal of Chemical Information and Modeling. (2025) DOI: 10.1021/acs.jcim.5c01971

Physics-based modeling medical chemistry

Liu, D., Song, T., Wang, S., Li, X., Han, P., Ju, G., Wang, J. and Wang, S.. DiffMeta-RL: Reinforcement Learning-Guided Graph Diffusion for Metabolically Stable Molecular Generation. Journal of Chemical Information and Modeling. (2025) DOI: 10.1021/acs.jcim.5c02060

medical chemistry

Liu, D., Song, T., Wang, S., Li, X., Han, P., Wang, J. and Wang, S.. AlphaPPIMI: A Comprehensive Deep Learning Framework for Predicting PPI-Modulator Interactions. Journal of Cheminformatics. (2025) DOI: 10.1186/s13321-025-01077-2

medical chemistry bioinformatics and cheminfo

Du, W., Zhang, S., Cai, Z., Li, X., Liu, Z., Fang, J., Wang, J., Wang, X. and Wang, Y.. Molecular Merged Hypergraph Neural Network for Explainable Solvation Free Energy Prediction. Research. (2025) DOI: 10.34133/research.0740

medical chemistry bioinformatics and cheminfo

Xiao, Y., Rodríguez‐Patón, A., Wang, J., Zheng, P., Ma, T., & Song, T.. Programmable DNA-based Molecular Neural Network Biocomputing Circuits for Solving Partial Differential Equations. Advanced Science. (2025) DOI: 10.1002/advs.202507060

bioinformatics and cheminfo Physics-based modeling

Zhou, P., Wang, J., Li, C., Wang, Z., Liu, Y., Sun, S., Lin, J., Wei, L., Cai, X., Lai, H. and Liu, W.. Instruction Multi-Constraint Molecular Generation Using a Teacher-Student Large Language Model. BMC Biology. (2025) DOI: 10.1186/s12915-025-02200-3

medical chemistry bioinformatics and cheminfo

Li, X., Cao, B., Wang, J., Meng, X., Wang, S., Huang, Y., Petretto, E. and Song, T.. Predicting mutation-disease associations through protein interactions via deep learning. IEEE Journal of Biomedical and Health Informatics. (2025) DOI: 10.1109/JBHI.2025.3541848

medical chemistry bioinformatics and cheminfo

Wang, J., Mao, J., Li, C., Xiang, H., Wang, X., Wang, S., Wang, Z., Chen, Y., Li, Y., No, K.T. and Song, T.. Interface-aware molecular generative framework for protein-protein interaction modulators. Journal of Cheminformatics. (2024) DOI: 10.1186/s13321-024-00930-0

medical chemistry design and optimization

Wang, J., Zhou, P., Wang, Z., Long, W., Chen, Y., No, K.T., Ouyang, D., Mao, J. and Zeng, X.. Diffusion-based generative drug-like molecular editing with chemical natural language. Journal of Pharmaceutical Analysis. (2024) DOI: 10.1016/j.jpha.2024.101137

medical chemistry design and optimization

Wang, J., Wang, X., Chu, Y., Li, C., Li, X., Meng, X., Fang, Y., No, K.T., Mao, J. and Zeng, X.. Exploring the conformational ensembles of protein-protein complex with transformer-based generative model. Journal of Chemical Theory and Computation. (2024) DOI: 10.1021/acs.jctc.4c00255

Physics-based modeling medical chemistry

Wang, M., Wang, J., Ji, J., Ma, C., Wang, H., He, J., Song, Y., Zhang, X., Cao, Y., Dai, Y. and Hua, M.. Improving compound-protein interaction prediction by focusing on intra-modality and inter-modality dynamics with a multimodal tensor fusion strategy. Computational and Structural Biotechnology Journal. (2024) DOI: 10.1016/j.csbj.2024.10.004

medical chemistry bioinformatics and cheminfo

Wang, S., Liang, D., Wang, J., Dong, K., Zhang, Y., Liang, H., Xu, X. and Song, T.. FraHMT: A fragment-oriented heterogeneous graph molecular generation model for target proteins. Journal of Chemical Information and Modeling. (2024) DOI: 10.1021/acs.jcim.4c00252

medical chemistry design and optimization

Gao, C., Bao, W., Wang, S., Zheng, J., Wang, L., Ren, Y., Jiao, L., Wang, J. and Wang, X.. DockingGA: Enhancing Targeted Molecule Generation using Transformer Neural Network and Genetic Algorithm with Docking Simulation. Briefings in functional genomics. (2024) DOI: 10.1093/bfgp/elae011

medical chemistry design and optimization

Jiang, L., Qu, S., Yu, Z., Wang, J. and Liu, X.. MOASL: Predicting drug mechanism of action through similarity learning with transcriptomic signature. Computers in Biology and Medicine. (2023) DOI: 10.1016/j.compbiomed.2023.107853

clinical pharmacy bioinformatics and cheminfo

Sun, H., Wang, J., Wu, H., Lin, S., Chen, J., Wei, J., Lv, S., Xiong, Y. and Wei, D.Q.. A multimodal deep learning framework for predicting PPI-modulator interactions. Journal of Chemical Information and Modeling. (2023) DOI: 10.1021/acs.jcim.3c01527

medical chemistry bioinformatics and cheminfo

Mao, J., Wang, J., Zeb, A., Cho, K.H., Jin, H., Kim, J., Lee, O., Wang, Y. and No, K.T.. Transformer-based molecular generative model for antiviral drug design. Journal of Chemical Information and Modeling. (2023) DOI: 10.1021/acs.jcim.3c00536

medical chemistry design and optimization

Wang, J., Mao, J., Wang, M., Le, X. and Wang, Y.. Explore drug-like space with deep generative models. Methods. (2023) DOI: 10.1016/j.ymeth.2023.01.004

medical chemistry design and optimization

Mao, J., Guan, S., Chen, Y., Zeb, A., Sun, Q., Lu, R., Dong, J., Wang, J. and Cao, D.. Application of a deep generative model produces novel and diverse functional peptides against microbial resistance. Computational and Structural Biotechnology Journal. (2022) DOI: 10.1016/j.csbj.2022.12.029

medical chemistry bioinformatics and cheminfo

Chu, Y., Zhang, Y., Wang, Q., Zhang, L., Wang, X., Wang, Y., Salahub, D.R., Xu, Q., Wang, J., Jiang, X. and Xiong, Y.. A transformer-based model to predict peptide–HLA class I binding and optimize mutated peptides for vaccine design. Nature Machine Intelligence. (2022) DOI: 10.1038/s42256-022-00459-7

design and optimization bioinformatics and cheminfo

Zhang, X., Wang, G., Meng, X., Wang, S., Zhang, Y., Rodriguez-Paton, A., Wang, J. and Wang, X.. Molormer: a lightweight self-attention-based method focused on spatial structure of molecular graph for drug–drug interactions prediction. Briefings in Bioinformatics. (2022) DOI: 10.1093/bib/bbac296

clinical pharmacy bioinformatics and cheminfo

Wang, J., Chu, Y., Mao, J., Jeon, H.N., Jin, H., Zeb, A., Jang, Y., Cho, K.H., Song, T. and No, K.T.. De novo molecular design with deep molecular generative models for PPI inhibitors. Briefings in Bioinformatics. (2022) DOI: 10.1093/bib/bbac285

medical chemistry design and optimization

Li, C., Yao, J., Wei, W., Niu, Z., Zeng, X., Li, J. and Wang, J.. Geometry-based molecular generation with deep constrained variational autoencoder. IEEE transactions on neural networks and learning systems. (2022) DOI: 10.1109/TNNLS.2022.3147790

medical chemistry design and optimization

Li, C., Wang, J., Niu, Z., Yao, J. and Zeng, X.. A spatial-temporal gated attention module for molecular property prediction based on molecular geometry. Briefings in Bioinformatics. (2021) DOI: 10.1093/bib/bbab078

medical chemistry design and optimization

Chen, Y., Ma, T., Yang, X., Wang, J., Song, B. and Zeng, X.. MUFFIN: multi-scale feature fusion for drug–drug interaction prediction. Bioinformatics. (2021) DOI: 10.1093/bioinformatics/btab169

clinical pharmacy bioinformatics and cheminfo

Qi, Z., Yang, G., Deng, T., Wang, J., Zhou, H., Popov, S.A.. Design and linkage optimization of ursane-thalidomide-based PROTACs and identification of their targeted-degradation properties to MDM2 protein. Bioorganic Chemistry. (2021) DOI: 10.1016/j.bioorg.2021.104901

clinical pharmacy bioinformatics and cheminfo