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)

Toward an understanding of the relation between gene regulation and 3D genome organization. - Hao Tian; Ying Yang 002; Sirui Liu 001; Hui Quan; Yi Qin Gao (Quant. Biol., 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)

Xponge: A Python package to perform pre- and post-processing of molecular simulations. - Yijie Xia; Yi Qin Gao (J. Open Source Softw., 2022)

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

Microscopic model on indoor propagation of respiratory droplets. - Manas Mondal; Srabani Chakrabarty; Yi Qin Gao; Dhananjay Bhattacharyya; Jaydeb Chakrabarti (Comput. Biol. Chem., 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)

Generating High-Precision Force Fields for Molecular Dynamics Simulations to Study Chemical Reaction Mechanisms using Molecular Configuration Transformer. - Sihao Yuan; Xu Han; Zhaoxin Xie; Cheng Fan; Yi Isaac Yang; Yi Qin Gao (CoRR, 2024)

DSDPFlex: Flexible-Receptor Docking with GPU Acceleration. - Chengwei Dong; Yupeng Huang; Xiaohan Lin; Hong Zhang; Yi Qin Gao (J. Chem. Inf. Model., 2024)

Integrated structure prediction of protein-protein docking with experimental restraints using ColabDock. - Shihao Feng; Zhenyu Chen; Chengwei Zhang; Yuhao Xie; Sergey Ovchinnikov 001; Yi Qin Gao; Sirui Liu 001 (Nat. Mac. Intell., 2024)

Author Correction: Integrated structure prediction of protein-protein docking with experimental restraints using ColabDock. - Shihao Feng; Zhenyu Chen; Chengwei Zhang; Yuhao Xie; Sergey Ovchinnikov 001; Yi Qin Gao; Sirui Liu 001 (Nat. Mac. Intell., 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)

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; Jun Zhang 069; Ziqiang Cao; Yi Qin Gao (CoRR, 2025)