Functional-Group-Based Diffusion for Pocket-Specific Molecule Generation and Elaboration. - Haitao Lin; Yufei Huang 002; Odin Zhang; Yunfan Liu 002; Lirong Wu; Siyuan Li 002; Zhiyuan Chen 008; Stan Z. Li (NeurIPS, 2023)

Protein 3D Graph Structure Learning for Robust Structure-based Protein Property Prediction. - Yufei Huang 002; Siyuan Li 002; Jin Su; Lirong Wu; Odin Zhang; Haitao Lin; Jingqi Qi; Zihan Liu; Zhangyang Gao; Yuyang Liu; Jiangbin Zheng 002; Stan Z. Li (CoRR, 2023)

Learning on topological surface and geometric structure for 3D molecular generation. - Odin Zhang; Tianyue Wang; Gaoqi Weng; Dejun Jiang 002; Ning Wang; Xiaorui Wang; Huifeng Zhao; Jialu Wu; Ercheng Wang; Guangyong Chen; Yafeng Deng; Peichen Pan; et al. (Nat. Comput. Sci., 2023)

Efficient and accurate large library ligand docking with KarmaDock. - Xujun Zhang; Odin Zhang; Chao Shen 008; Wanglin Qu; Shicheng Chen; Hanqun Cao; Yu Kang 002; Zhe Wang 041; Ercheng Wang; Jintu Zhang; Yafeng Deng; Furui Liu; et al. (Nat. Comput. Sci., 2023)

ResGen is a pocket-aware 3D molecular generation model based on parallel multiscale modelling. - Odin Zhang; Jintu Zhang; Jieyu Jin; Xujun Zhang; Renling Hu; Chao Shen 008; Hanqun Cao; Hongyan Du; Yu Kang 002; Yafeng Deng; Furui Liu; Guangyong Chen; et al. (Nat. Mac. Intell., 2023)

Protein 3D Graph Structure Learning for Robust Structure-Based Protein Property Prediction. - Yufei Huang 002; Siyuan Li 002; Lirong Wu; Jin Su; Haitao Lin; Odin Zhang; Zihan Liu; Zhangyang Gao; Jiangbin Zheng 002; Stan Z. Li (AAAI, 2024)

Re-Dock: Towards Flexible and Realistic Molecular Docking with Diffusion Bridge. - Yufei Huang 002; Odin Zhang; Lirong Wu; Cheng Tan 012; Haitao Lin; Zhangyang Gao; Siyuan Li 002; Stan Z. Li (ICML, 2024)

GeoAB: Towards Realistic Antibody Design and Reliable Affinity Maturation. - Haitao Lin; Lirong Wu; Yufei Huang 002; Yunfan Liu 002; Odin Zhang; Yuanqing Zhou; Rui Sun; Stan Z. Li (ICML, 2024)

PPFLOW: Target-Aware Peptide Design with Torsional Flow Matching. - Haitao Lin; Odin Zhang; Huifeng Zhao; Dejun Jiang 002; Lirong Wu; Zicheng Liu 006; Yufei Huang 002; Stan Z. Li (ICML, 2024)

Rethinking the Diffusion Models for Missing Data Imputation: A Gradient Flow Perspective. - Zhichao Chen 001; Haoxuan Li 001; Fangyikang Wang; Odin Zhang; Hu Xu; Xiaoyu Jiang; Zhihuan Song; Hao Wang 049 (NeurIPS, 2024)

Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency. - Tianyue Wang; Langcheng Wang; Xujun Zhang; Chao Shen 008; Odin Zhang; Jike Wang; Jialu Wu; Ruofan Jin; Donghao Zhou; Shicheng Chen; Liwei Liu; Xiaorui Wang; et al. (Briefings Bioinform., 2024)

Deep Geometry Handling and Fragment-wise Molecular 3D Graph Generation. - Odin Zhang; Yufei Huang 002; Shichen Cheng; Mengyao Yu; Xujun Zhang; Haitao Lin; Yundian Zeng; Mingyang Wang 004; Zhenxing Wu; Huifeng Zhao; Zaixi Zhang; Chenqing Hua; et al. (CoRR, 2024)

Deep Lead Optimization: Leveraging Generative AI for Structural Modification. - Odin Zhang; Haitao Lin; Hui Zhang; Huifeng Zhao; Yufei Huang 002; Yuansheng Huang; Dejun Jiang 002; Chang-Yu Hsieh; Peichen Pan; Tingjun Hou (CoRR, 2024)

CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph. - Haitao Lin; Guojiang Zhao; Odin Zhang; Yufei Huang 002; Lirong Wu; Zicheng Liu 006; Siyuan Li 002; Cheng Tan 012; Zhifeng Gao; Stan Z. Li (CoRR, 2024)

Rethinking the Diffusion Models for Numerical Tabular Data Imputation from the Perspective of Wasserstein Gradient Flow. - Zhichao Chen 001; Haoxuan Li 001; Fangyikang Wang; Odin Zhang; Hu Xu; Xiaoyu Jiang; Zhihuan Song; Eric H. Wang (CoRR, 2024)

Token-Mol 1.0: Tokenized drug design with large language model. - Jike Wang; Rui Qin; Mingyang Wang 004; Meijing Fang; Yangyang Zhang; Yuchen Zhu; Qun Su; Qiaolin Gou; Chao Shen 008; Odin Zhang; Zhenxing Wu; Dejun Jiang 002; et al. (CoRR, 2024)

EnzymeFlow: Generating Reaction-specific Enzyme Catalytic Pockets through Flow Matching and Co-Evolutionary Dynamics. - Chenqing Hua; Yong Liu; Dinghuai Zhang; Odin Zhang; Sitao Luan; Kevin K. Yang; Guy Wolf; Doina Precup; Shuangjia Zheng (CoRR, 2024)

Reaction-conditioned De Novo Enzyme Design with GENzyme. - Chenqing Hua; Jiarui Lu; Yong Liu; Odin Zhang; Jian Tang 005; Rex Ying; Wengong Jin; Guy Wolf; Doina Precup; Shuangjia Zheng (CoRR, 2024)

DrugFlow: An AI-Driven One-Stop Platform for Innovative Drug Discovery. - Chao Shen 008; Jianfei Song; Chang-Yu Hsieh; Dong-Sheng Cao 001; Yu Kang 002; Wenling Ye; Zhenxing Wu; Jike Wang; Odin Zhang; Xujun Zhang; Hao Zeng; Heng Cai; et al. (J. Chem. Inf. Model., 2024)

Leveraging language model for advanced multiproperty molecular optimization via prompt engineering. - Zhenxing Wu; Odin Zhang; Xiaorui Wang; Li Fu; Huifeng Zhao; Jike Wang; Hongyan Du; Dejun Jiang 002; Yafeng Deng; Dong-Sheng Cao 001; Chang-Yu Hsieh; Tingjun Hou (Nat. Mac. Intell., 2024)

EVA: Geometric Inverse Design for Fast Protein Motif-Scaffolding with Coupled Flow. - Yufei Huang 002; Yunshu Liu; Lirong Wu; Haitao Lin; Cheng Tan 012; Odin Zhang; Zhangyang Gao; Siyuan Li 002; Zicheng Liu 006; Yunfan Liu 002; Tailin Wu; Stan Z. Li (ICLR, 2025)

CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph. - Haitao Lin; Guojiang Zhao; Odin Zhang; Yufei Huang 002; Lirong Wu; Cheng Tan 012; Zicheng Liu 006; Zhifeng Gao; Stan Z. Li (ICLR, 2025)

Durian: A Comprehensive Benchmark for Structure-Based 3D Molecular Generation. - Dou Nie; Huifeng Zhao; Odin Zhang; Gaoqi Weng; Hui Zhang; Jieyu Jin; Haitao Lin; Yufei Huang 002; Liwei Liu; Dan Li 013; Tingjun Hou; Yu Kang 002 (J. Chem. Inf. Model., 2025)

Deep lead optimization enveloped in protein pocket and its application in designing potent and selective ligands targeting LTK protein. - Shicheng Chen; Odin Zhang; Chenran Jiang; Huifeng Zhao; Xujun Zhang; Mengting Chen; Yun Liu; Qun Su; Zhenxing Wu; Xinyue Wang; Wanglin Qu; Yuanyi Ye; et al. (Nat. Mac. Intell., 2025)

Tokenizing Electron Cloud in Protein-Ligand Interaction Learning. - Haitao Lin; Odin Zhang; Jia Xu; Yunfan Liu 002; Zheng Chen 014; Lirong Wu; Yufei Huang 002; Zhifeng Gao; Stan Z. Li (CoRR, 2025)

Graph Neural Networks in Modern AI-aided Drug Discovery. - Odin Zhang; Haitao Lin; Xujun Zhang; Xiaorui Wang; Zhenxing Wu; Qing Ye; Weibo Zhao; Jike Wang; Kejun Ying; Yu Kang 002; Chang-Yu Hsieh; Tingjun Hou (CoRR, 2025)