A Perspective on Deep Learning for Molecular Modeling and Simulations. - Jun Zhang 071; Yao-Kun Lei; Zhen Zhang; Junhan Chang; Maodong Li; Xu Han; Lijiang Yang; Yi Isaac Yang; Yi Qin Gao (CoRR, 2020)

Deep Reinforcement Learning of Transition States. - Jun Zhang 071; Yao-Kun Lei; Zhen Zhang; Xu Han; Maodong Li; Lijiang Yang; Yi Isaac Yang; Yi Qin Gao (CoRR, 2020)

Molecular CT: Unifying Geometry and Representation Learning for Molecules at Different Scales. - Jun Zhang 071; Yaqiang Zhou; Yao-Kun Lei; Yi Isaac Yang; Yi Qin Gao (CoRR, 2020)

PSP: Million-level Protein Sequence Dataset for Protein Structure Prediction. - Sirui Liu 001; Jun Zhang 071; Haotian Chu; Min Wang 037; Boxin Xue; Ningxi Ni; Jialiang Yu; Yuhao Xie; Zhenyu Chen; Mengyun Chen; Yuan Liu; Piya Patra; et al. (CoRR, 2022)

Few-Shot Learning of Accurate Folding Landscape for Protein Structure Prediction. - Jun Zhang 071; Sirui Liu 001; Mengyun Chen; Haotian Chu; Min Wang 037; Zidong Wang 010; Jialiang Yu; Ningxi Ni; Fan Yu; Diqing Chen; Yi Isaac Yang; Boxin Xue; et al. (CoRR, 2022)

Machine-Learned Invertible Coarse Graining for Multiscale Molecular Modeling. - Jun Zhang 071; Xiaohan Lin; Weinan E; Yi Qin Gao (CoRR, 2023)

DSDP: A Blind Docking Strategy Accelerated by GPUs. - Yupeng Huang; Hong Zhang; Siyuan Jiang; Dajiong Yue; Xiaohan Lin; Jun Zhang 071; Yi Qin Gao (J. Chem. Inf. Model., 2023)

Versatile Framework for Drug-Target Interaction Prediction by Considering Domain-Specific Features. - Shuo Liu; Jialiang Yu; Ningxi Ni; Zidong Wang 010; Mengyun Chen; Yuquan Li; Chen Xu; Yahao Ding; Jun Zhang 071; Xiaojun Yao; Huanxiang Liu (J. Chem. Inf. Model., 2024)

ProtTeX: Structure-In-Context Reasoning and Editing of Proteins with Large Language Models. - Zicheng Ma; Chuanliu Fan; Zhicong Wang; Zhenyu Chen; Xiaohan Lin; Yanheng Li; Shihao Feng; Ziqiang Cao; Jun Zhang 071; Yi Qin Gao (J. Chem. Inf. Model., 2025)