Selected Publications
* indicates equal contribution; † indicates corresponding author.
Sequence-based Drug-Target Complex Pre-training Enhances Protein-Ligand Binding Process Predictions Tackling Crypticity
Shuo Zhang, Li Xie, Daniel Tiourine, Lei Xie
Preprint, 2025.
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.
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.
A Universal Framework for Accurate and Efficient Geometric Deep Learning of Molecular Systems
Shuo Zhang, Yang Liu, Lei Xie
Scientific Reports, 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.
TrustAffinity: Accurate, Reliable, and Scalable Out-of-Distribution Protein–Ligand Binding Affinity Prediction Using Trustworthy Deep Learning
Amitesh Badkul, Li Xie, Shuo Zhang, Lei Xie
Neural Information Processing Systems (NeurIPS) New Frontiers of AI for Drug Discovery and Development (AI4D3) Workshop, 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.
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.