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2020 – today
- 2025
[j7]Dou Nie, Huifeng Zhao, Odin Zhang, Gaoqi Weng, Hui Zhang, Jieyu Jin, Haitao Lin, Yufei Huang, Liwei Liu, Dan Li
, Tingjun Hou, Yu Kang:
Durian: A Comprehensive Benchmark for Structure-Based 3D Molecular Generation. J. Chem. Inf. Model. 65(1): 173-186 (2025)- [j6]Shicheng Chen, Odin Zhang, Chenran Jiang, Huifeng Zhao, Xujun Zhang, Mengting Chen, Yun Liu, Qun Su, Zhenxing Wu, Xinyue Wang, Wanglin Qu, Yuanyi Ye, Xin Chai, Ning Wang, Tianyue Wang, Yuan An, Guanlin Wu, Qianqian Yang, Jiean Chen, Wei Xie, Haitao Lin, Dan Li, Chang-Yu Hsieh, Yong Huang, Yu Kang, Tingjun Hou, Peichen Pan:
Deep lead optimization enveloped in protein pocket and its application in designing potent and selective ligands targeting LTK protein. Nat. Mac. Intell. 7(3): 448-458 (2025) - [c8]Yufei Huang, Yunshu Liu, Lirong Wu, Haitao Lin, Cheng Tan, Odin Zhang, Zhangyang Gao, Siyuan Li, Zicheng Liu, Yunfan Liu, Tailin Wu, Stan Z. Li:
EVA: Geometric Inverse Design for Fast Protein Motif-Scaffolding with Coupled Flow. ICLR 2025 - [c7]Haitao Lin, Guojiang Zhao, Odin Zhang, Yufei Huang, Lirong Wu, Cheng Tan, Zicheng Liu, Zhifeng Gao, Stan Z. Li:
CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph. ICLR 2025 - 2024
- [j5]Chao Shen, Jianfei Song, Chang-Yu Hsieh, Dong-Sheng Cao, Yu Kang, Wenling Ye, Zhenxing Wu, Jike Wang, Odin Zhang, Xujun Zhang, Hao Zeng, Heng Cai, Yu Chen, Linkang Chen, Hao Luo, Xinda Zhao, Tianye Jian, Tong Chen, Dejun Jiang, Mingyang Wang, Qing Ye, Jialu Wu, Hongyan Du, Hui Shi, Yafeng Deng, Tingjun Hou:
DrugFlow: An AI-Driven One-Stop Platform for Innovative Drug Discovery. J. Chem. Inf. Model. 64(14): 5381-5391 (2024) - [j4]Zhenxing Wu, Odin Zhang, Xiaorui Wang, Li Fu, Huifeng Zhao, Jike Wang, Hongyan Du, Dejun Jiang, Yafeng Deng, Dong-Sheng Cao, Chang-Yu Hsieh, Tingjun Hou:
Leveraging language model for advanced multiproperty molecular optimization via prompt engineering. Nat. Mac. Intell. 6(11): 1359-1369 (2024) - [c6]Yufei Huang, Siyuan Li, Lirong Wu, Jin Su, Haitao Lin, Odin Zhang, Zihan Liu, Zhangyang Gao, Jiangbin Zheng, Stan Z. Li:
Protein 3D Graph Structure Learning for Robust Structure-Based Protein Property Prediction. AAAI 2024: 12662-12670 - [c5]Yufei Huang, Odin Zhang, Lirong Wu, Cheng Tan, Haitao Lin, Zhangyang Gao, Siyuan Li, Stan Z. Li:
Re-Dock: Towards Flexible and Realistic Molecular Docking with Diffusion Bridge. ICML 2024 - [c4]Haitao Lin, Lirong Wu, Yufei Huang, Yunfan Liu, Odin Zhang, Yuanqing Zhou, Rui Sun, Stan Z. Li:
GeoAB: Towards Realistic Antibody Design and Reliable Affinity Maturation. ICML 2024 - [c3]Haitao Lin, Odin Zhang, Huifeng Zhao, Dejun Jiang, Lirong Wu, Zicheng Liu, Yufei Huang, Stan Z. Li:
PPFLOW: Target-Aware Peptide Design with Torsional Flow Matching. ICML 2024 - [c2]Zhichao Chen, Haoxuan Li, Fangyikang Wang, Odin Zhang, Hu Xu, Xiaoyu Jiang, Zhihuan Song, Hao Wang:
Rethinking the Diffusion Models for Missing Data Imputation: A Gradient Flow Perspective. NeurIPS 2024 - [i10]Yufei Huang, Odin Zhang, Lirong Wu, Cheng Tan, Haitao Lin, Zhangyang Gao, Siyuan Li, Stan Z. Li:
Re-Dock: Towards Flexible and Realistic Molecular Docking with Diffusion Bridge. CoRR abs/2402.11459 (2024) - [i9]Odin Zhang, Yufei Huang, Shichen Cheng, Mengyao Yu, Xujun Zhang, Haitao Lin, Yundian Zeng, Mingyang Wang, Zhenxing Wu, Huifeng Zhao, Zaixi Zhang, Chenqing Hua, Yu Kang, Sunliang Cui, Peichen Pan, Chang-Yu Hsieh, Tingjun Hou:
Deep Geometry Handling and Fragment-wise Molecular 3D Graph Generation. CoRR abs/2404.00014 (2024) - [i8]Odin Zhang, Haitao Lin, Hui Zhang, Huifeng Zhao, Yufei Huang, Yuansheng Huang, Dejun Jiang, Chang-Yu Hsieh, Peichen Pan, Tingjun Hou:
Deep Lead Optimization: Leveraging Generative AI for Structural Modification. CoRR abs/2404.19230 (2024) - [i7]Haitao Lin, Odin Zhang, Huifeng Zhao, Dejun Jiang, Lirong Wu, Zicheng Liu, Yufei Huang, Stan Z. Li:
PPFlow: Target-aware Peptide Design with Torsional Flow Matching. CoRR abs/2405.06642 (2024) - [i6]Haitao Lin, Guojiang Zhao, Odin Zhang, Yufei Huang, Lirong Wu, Zicheng Liu, Siyuan Li, Cheng Tan, Zhifeng Gao, Stan Z. Li:
CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph. CoRR abs/2406.10840 (2024) - [i5]Zhichao Chen, Haoxuan Li, Fangyikang Wang, Odin Zhang, Hu Xu, Xiaoyu Jiang, Zhihuan Song, Eric H. Wang:
Rethinking the Diffusion Models for Numerical Tabular Data Imputation from the Perspective of Wasserstein Gradient Flow. CoRR abs/2406.15762 (2024) - [i4]Jike Wang, Rui Qin, Mingyang Wang, Meijing Fang, Yangyang Zhang, Yuchen Zhu, Qun Su, Qiaolin Gou, Chao Shen, Odin Zhang, Zhenxing Wu, Dejun Jiang, Xujun Zhang, Huifeng Zhao, Xiaozhe Wan, Zhourui Wu, Liwei Liu, Yu Kang, Chang-Yu Hsieh, Tingjun Hou:
Token-Mol 1.0: Tokenized drug design with large language model. CoRR abs/2407.07930 (2024) - [i3]Chenqing Hua, Yong Liu, Dinghuai Zhang, Odin Zhang, Sitao Luan, Kevin K. Yang, Guy Wolf, Doina Precup, Shuangjia Zheng:
EnzymeFlow: Generating Reaction-specific Enzyme Catalytic Pockets through Flow Matching and Co-Evolutionary Dynamics. CoRR abs/2410.00327 (2024) - [i2]Chenqing Hua, Jiarui Lu, Yong Liu, Odin Zhang, Jian Tang, Rex Ying, Wengong Jin, Guy Wolf, Doina Precup, Shuangjia Zheng:
Reaction-conditioned De Novo Enzyme Design with GENzyme. CoRR abs/2411.16694 (2024) - 2023
- [j3]Odin Zhang, Jintu Zhang, Jieyu Jin, Xujun Zhang, Renling Hu, Chao Shen, Hanqun Cao, Hongyan Du, Yu Kang, Yafeng Deng, Furui Liu, Guangyong Chen, Chang-Yu Hsieh, Tingjun Hou:
ResGen is a pocket-aware 3D molecular generation model based on parallel multiscale modelling. Nat. Mac. Intell. 5(9): 1020-1030 (2023) - [j2]Xujun Zhang, Odin Zhang, Chao Shen, Wanglin Qu, Shicheng Chen, Hanqun Cao, Yu Kang, Zhe Wang, Ercheng Wang, Jintu Zhang, Yafeng Deng, Furui Liu, Tianyue Wang, Hongyan Du, Langcheng Wang, Peichen Pan, Guangyong Chen, Chang-Yu Hsieh, Tingjun Hou:
Efficient and accurate large library ligand docking with KarmaDock. Nat. Comput. Sci. 3(9): 789-804 (2023) - [j1]Odin Zhang, Tianyue Wang, Gaoqi Weng, Dejun Jiang, Ning Wang, Xiaorui Wang, Huifeng Zhao, Jialu Wu, Ercheng Wang, Guangyong Chen, Yafeng Deng, Peichen Pan, Yu Kang, Chang-Yu Hsieh, Tingjun Hou:
Learning on topological surface and geometric structure for 3D molecular generation. Nat. Comput. Sci. 3(10): 849-859 (2023) - [c1]Haitao Lin, Yufei Huang, Odin Zhang, Yunfan Liu, Lirong Wu, Siyuan Li, Zhiyuan Chen, Stan Z. Li:
Functional-Group-Based Diffusion for Pocket-Specific Molecule Generation and Elaboration. NeurIPS 2023 - [i1]Yufei Huang, Siyuan Li, Jin Su, Lirong Wu, Odin Zhang, Haitao Lin, Jingqi Qi, Zihan Liu, Zhangyang Gao, Yuyang Liu, Jiangbin Zheng, Stan Z. Li:
Protein 3D Graph Structure Learning for Robust Structure-based Protein Property Prediction. CoRR abs/2310.11466 (2023)
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