Selected Publications

Sequence-based Drug-Target Binding Site Pre-training Enables Cryptic Pocket Detection and Improves Binding Affinity and Kinetics Prediction
Shuo Zhang†, Li Xie, Daniel Tiourine, Lei Xie†

Journal of Cheminformatics, 2026 (Impact Factor: 7.9).

Multimodal Out-of-Distribution Individual Uncertainty Quantification Enhances Binding Affinity Prediction for Polypharmacology
Amitesh Badkul, Li Xie, Shuo Zhang, Lei Xie

Nature Machine Intelligence, 2025 (Impact Factor: 29.8).

MolGene-E: Inverse Molecular Design to Modulate Single Cell Transcriptomics
Rahul Ohlan, Raswanth Murugan, Li Xie, Mohammadsadeq Mottaqi, Shuo Zhang†, Lei Xie†

International Conference on Machine Learning (ICML) AI4Science Workshop, 2024.

Protein Language Model-Powered 3D Ligand Binding Site Prediction from Protein Sequence
Shuo Zhang, Lei Xie

Neural Information Processing Systems (NeurIPS) AI for Science Workshop, 2023.

A Universal Framework for Accurate and Efficient Geometric Deep Learning of Molecular Systems
Shuo Zhang, Yang Liu, Lei Xie

Scientific Reports, 2023.

End-to-End Sequence-Structure-Function Meta-Learning Predicts Genome-Wide Chemical-Protein Interactions for Dark Proteins
Tian Cai, Li Xie, Shuo Zhang, Muge Chen, Di He, Amitesh Badkul, Yang Liu, Hari Krishna Namballa, Michael Dorogan, Wayne W. Harding, Cameron Mura, Philip E. Bourne, Lei Xie

PLOS Computational Biology, 2023.

Physics-aware Graph Neural Network for Accurate RNA 3D Structure Prediction
Shuo Zhang, Yang Liu, Lei Xie

Neural Information Processing Systems (NeurIPS) Machine Learning for Structural Biology (MLSB) Workshop, 2022.

Molecular Mechanics-Driven Graph Neural Network with Multiplex Graph for Molecular Structures
Shuo Zhang, Yang Liu, Lei Xie

Neural Information Processing Systems (NeurIPS) Machine Learning for Structural Biology (MLSB) Workshop, 2020.

Improving Attention Mechanism in Graph Neural Networks via Cardinality Preservation
Shuo Zhang, Lei Xie

International Joint Conference on Artificial Intelligence (IJCAI), 2020.

Acceptance rate: 592/4717=12.6%.

Heterogeneous Multi-Layered Network Model for Omics Data Integration and Analysis
Bohyun Lee, Shuo Zhang, Aleksandar Poleksic, Lei Xie

Frontiers in Genetics, 2020.

Theoretical Study of Adsorption and Dehydrogenation of C2H4 on Cu(410)
Yangyunli Sun*, Shuo Zhang*, Wenhua Zhang, Zhenyu Li

Chinese Journal of Chemical Physics, 2018.