Chang-Yu Hsieh (Changyu Hsieh)

Publication Activity (10 Years)

Years Active: 2022-2024
Publications (10 Years): 34

Top Topics

Molecular Dynamics Simulations

Top Venues

Nature communications

Nature computational science

Chemical science

Journal of chemical information and modeling

This page only lists publications with an associated author ORCID identifier.

Publications

Xiaorui Wang, Xiaodan Yin, De-Jun Jiang, Huifeng Zhao, Zhenxing Wu, Odin Zhang, Jike Wang, Yuquan Li, Yafeng Deng, Huanxiang Liu, Pei Luo, Yuqiang Han, Ting-Jun Hou, Xiaojun Yao, Chang-Yu Hsieh
Multi-modal deep learning enables efficient and accurate annotation of enzymatic active sites. Nature communications 15 (1) (2024)
Yuqiang Han, Xiaoyang Xu, Chang-Yu Hsieh, Keyan Ding, Hongxia Xu, Renjun Xu, Ting-Jun Hou, Qiang Zhang, Huajun Chen
Retrosynthesis prediction with an iterative string editing model. Nature communications 15 (1) (2024)
Jiacai Yi, Shaohua Shi, Li Fu, Ziyi Yang, Pengfei Nie, Ai-Ping Lu, Chengkun Wu, Yafeng Deng, Chang-Yu Hsieh, Xiangxiang Zeng, Ting-Jun Hou, Dongsheng Cao
OptADMET: a web-based tool for substructure modifications to improve ADMET properties of lead compounds. Nature protocols (2024)
Jie Yue, Bingxin Peng, Yu Chen, Jieyu Jin, Xinda Zhao, Chao Shen, Xiangyang Ji, Chang-Yu Hsieh, Jianfei Song, Ting-Jun Hou, Yafeng Deng, Jike Wang
Unlocking comprehensive molecular design across all scenarios with large language model and unordered chemical language. Chemical science 15 (34) (2024)
Dejun Jiang, Hongyan Du, Huifeng Zhao, Yafeng Deng, Zhenxing Wu, Jike Wang, Yundian Zeng, Haotian Zhang, Xiaorui Wang, Ercheng Wang, Ting-Jun Hou, Chang-Yu Hsieh
Assessing the performance of MM/PBSA and MM/GBSA methods. 10. Prediction reliability of binding affinities and binding poses for RNA-ligand complexes. Physical chemistry chemical physics : PCCP 26 (13) (2024)
Dejun Jiang, Hongyan Du, Huifeng Zhao, Yafeng Deng, Zhenxing Wu, Jike Wang, Yundian Zeng, Haotian Zhang, Xiaorui Wang, Ercheng Wang, Ting-Jun Hou, Chang-Yu Hsieh
Assessing the performance of MM/PBSA and MM/GBSA methods. 10. Prediction reliability of binding affinities and binding poses for RNA-ligand complexes. Physical chemistry chemical physics : PCCP 26 (13) (2024)
Dejun Jiang, Hongyan Du, Huifeng Zhao, Yafeng Deng, Zhenxing Wu, Jike Wang, Yundian Zeng, Haotian Zhang, Xiaorui Wang, Ercheng Wang, Ting-Jun Hou, Chang-Yu Hsieh
Assessing the performance of MM/PBSA and MM/GBSA methods. 10. Prediction reliability of binding affinities and binding poses for RNA-ligand complexes. Physical chemistry chemical physics : PCCP (2024)
Yuqiang Han, Xiaoyang Xu, Chang-Yu Hsieh, Keyan Ding, Hongxia Xu, Renjun Xu, Ting-Jun Hou, Qiang Zhang, Huajun Chen
Retrosynthesis prediction with an iterative string editing model. Nature communications 15 (1) (2024)
Jiacai Yi, Shaohua Shi, Li Fu, Ziyi Yang, Pengfei Nie, Ai-Ping Lu, Chengkun Wu, Yafeng Deng, Chang-Yu Hsieh, Xiangxiang Zeng, Ting-Jun Hou, Dongsheng Cao
OptADMET: a web-based tool for substructure modifications to improve ADMET properties of lead compounds. Nature protocols 19 (4) (2024)
Yuqiang Han, Xiaoyang Xu, Chang-Yu Hsieh, Keyan Ding, Hongxia Xu, Renjun Xu, Ting-Jun Hou, Qiang Zhang, Huajun Chen
Retrosynthesis prediction with an iterative string editing model. Nature communications 15 (1) (2024)
Xiaorui Wang, Xiaodan Yin, De-Jun Jiang, Huifeng Zhao, Zhenxing Wu, Odin Zhang, Jike Wang, Yuquan Li, Yafeng Deng, Huanxiang Liu, Pei Luo, Yuqiang Han, Ting-Jun Hou, Xiaojun Yao, Chang-Yu Hsieh
Multi-modal deep learning enables efficient and accurate annotation of enzymatic active sites. Nature communications 15 (1) (2024)
Jiacai Yi, Shaohua Shi, Li Fu, Ziyi Yang, Pengfei Nie, Ai-Ping Lu, Chengkun Wu, Yafeng Deng, Chang-Yu Hsieh, Xiangxiang Zeng, Ting-Jun Hou, Dongsheng Cao
OptADMET: a web-based tool for substructure modifications to improve ADMET properties of lead compounds. Nature protocols 19 (4) (2024)
Heng Cai, Chao Shen, Tianye Jian, Xujun Zhang, Tong Chen, Xiaoqi Han, Zhuo Yang, Wei Dang, Chang-Yu Hsieh, Yu Kang, Peichen Pan, Xiangyang Ji, Jianfei Song, Ting-Jun Hou, Yafeng Deng
CarsiDock: a deep learning paradigm for accurate protein-ligand docking and screening based on large-scale pre-training. Chemical science 15 (4) (2023)
Heng Cai, Chao Shen, Tianye Jian, Xujun Zhang, Tong Chen, Xiaoqi Han, Zhuo Yang, Wei Dang, Chang-Yu Hsieh, Yu Kang, Peichen Pan, Xiangyang Ji, Jianfei Song, Ting-Jun Hou, Yafeng Deng
CarsiDock: a deep learning paradigm for accurate protein-ligand docking and screening based on large-scale pre-training. Chemical science 15 (4) (2023)
Tiantao Liu, Zheng Cao, Yuansheng Huang, Yue Wan, Jian Wu, Chang-Yu Hsieh, Ting-Jun Hou, Yu Kang
SynCluster: Reaction Type Clustering and Recommendation Framework for Synthesis Planning. JACS Au 3 (12) (2023)
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, Ting-Jun Hou
Efficient and accurate large library ligand docking with KarmaDock. Nature computational science 3 (9) (2023)
Zhenxing Wu, Jike Wang, Hongyan Du, De-Jun Jiang, Yu Kang, Dan Li, Peichen Pan, Yafeng Deng, Dong-Sheng Cao, Chang-Yu Hsieh, Ting-Jun Hou
Chemistry-intuitive explanation of graph neural networks for molecular property prediction with substructure masking. Nature communications 14 (1) (2023)
Zhenxing Wu, Jike Wang, Hongyan Du, De-Jun Jiang, Yu Kang, Dan Li, Peichen Pan, Yafeng Deng, Dong-Sheng Cao, Chang-Yu Hsieh, Ting-Jun Hou
Chemistry-intuitive explanation of graph neural networks for molecular property prediction with substructure masking. Nature communications 14 (1) (2023)
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, Ting-Jun Hou
Efficient and accurate large library ligand docking with KarmaDock. Nature computational science 3 (9) (2023)
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, Ting-Jun Hou
Efficient and accurate large library ligand docking with KarmaDock. Nature computational science 3 (9) (2023)
Zhenxing Wu, Jike Wang, Hongyan Du, De-Jun Jiang, Yu Kang, Dan Li, Peichen Pan, Yafeng Deng, Dong-Sheng Cao, Chang-Yu Hsieh, Ting-Jun Hou
Chemistry-intuitive explanation of graph neural networks for molecular property prediction with substructure masking. Nature communications 14 (1) (2023)
Zhenxing Wu, Jike Wang, Hongyan Du, De-Jun Jiang, Yu Kang, Dan Li, Peichen Pan, Yafeng Deng, Dong-Sheng Cao, Chang-Yu Hsieh, Ting-Jun Hou
Chemistry-intuitive explanation of graph neural networks for molecular property prediction with substructure masking. Nature communications 14 (1) (2023)
Zhenxing Wu, Jike Wang, Hongyan Du, De-Jun Jiang, Yu Kang, Dan Li, Peichen Pan, Yafeng Deng, Dong-Sheng Cao, Chang-Yu Hsieh, Ting-Jun Hou
Chemistry-intuitive explanation of graph neural networks for molecular property prediction with substructure masking. Nature communications 14 (1) (2023)
Zaixi Zhang, Qi Liu, Chee-Kong Lee, Chang-Yu Hsieh, Enhong Chen
An equivariant generative framework for molecular graph-structure Co-design. Chemical science 14 (31) (2023)
Chao Shen, Xujun Zhang, Chang-Yu Hsieh, Yafeng Deng, Dong Wang, Lei Xu, Jian Wu, Dan Li, Yu Kang, Ting-Jun Hou, Peichen Pan
A generalized protein-ligand scoring framework with balanced scoring, docking, ranking and screening powers. Chemical science 14 (30) (2023)
Tiantao Liu, Zheng Cao, Yuansheng Huang, Yue Wan, Jian Wu, Chang-Yu Hsieh, Ting-Jun Hou, Yu Kang
SynCluster: Reaction Type Clustering and Recommendation Framework for Synthesis Planning. JACS Au 3 (12) (2023)
Jike Wang, Yundian Zeng, Huiyong Sun, Junmei Wang, Xiaorui Wang, Ruofan Jin, Mingyang Wang, Xujun Zhang, Dong-Sheng Cao, Xi Chen, Chang-Yu Hsieh, Ting-Jun Hou
Molecular Generation with Reduced Labeling through Constraint Architecture. Journal of chemical information and modeling (2023)
Odin Zhang, Tianyue Wang, Gaoqi Weng, De-Jun Jiang, Ning Wang, Xiaorui Wang, Huifeng Zhao, Jialu Wu, Ercheng Wang, Guangyong Chen, Yafeng Deng, Peichen Pan, Yu Kang, Chang-Yu Hsieh, Ting-Jun Hou
Learning on topological surface and geometric structure for 3D molecular generation. Nature computational science 3 (10) (2023)
Odin Zhang, Tianyue Wang, Gaoqi Weng, De-Jun Jiang, Ning Wang, Xiaorui Wang, Huifeng Zhao, Jialu Wu, Ercheng Wang, Guangyong Chen, Yafeng Deng, Peichen Pan, Yu Kang, Chang-Yu Hsieh, Ting-Jun Hou
Learning on topological surface and geometric structure for 3D molecular generation. Nature computational science 3 (10) (2023)
Tiantao Liu, Zheng Cao, Yuansheng Huang, Yue Wan, Jian Wu, Chang-Yu Hsieh, Ting-Jun Hou, Yu Kang
SynCluster: Reaction Type Clustering and Recommendation Framework for Synthesis Planning. JACS Au 3 (12) (2023)
Yan-Jing Duan, Li Fu, Xiao-Chen Zhang, Teng-Zhi Long, Yuan-Hang He, Zhao-Qian Liu, Ai-Ping Lu, Ya-Feng Deng, Chang-Yu Hsieh, Ting-Jun Hou, Dong-Sheng Cao
Improved GNNs for Log  D 7.4 Prediction by Transferring Knowledge from Low-Fidelity Data. Journal of chemical information and modeling (2023)
Zhenxing Wu, Jihong Chen, Yitong Li, Yafeng Deng, Haitao Zhao, Chang-Yu Hsieh, Ting-Jun Hou
From Black Boxes to Actionable Insights: A Perspective on Explainable Artificial Intelligence for Scientific Discovery. Journal of chemical information and modeling (2023)
Odin Zhang, Tianyue Wang, Gaoqi Weng, De-Jun Jiang, Ning Wang, Xiaorui Wang, Huifeng Zhao, Jialu Wu, Ercheng Wang, Guangyong Chen, Yafeng Deng, Peichen Pan, Yu Kang, Chang-Yu Hsieh, Ting-Jun Hou
Learning on topological surface and geometric structure for 3D molecular generation. Nature computational science 3 (10) (2023)
Jialu Wu, Junmei Wang, Zhenxing Wu, Shengyu Zhang, Yafeng Deng, Yu Kang, Dong-Sheng Cao, Chang-Yu Hsieh, Ting-Jun Hou
ALipSol: An Attention-Driven Mixture-of-Experts Model for Lipophilicity and Solubility Prediction. Journal of chemical information and modeling (2022)