Peichen Pan

Publication Activity (10 Years)

Years Active: 2022-2024
Publications (10 Years): 36

Top Topics

Molecular Dynamics Simulations

Top Venues

Journal of medicinal chemistry

Nature computational science

Nature communications

Journal of chemical information and modeling

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

Publications

Tianyue Wang, Langcheng Wang, Xujun Zhang, Chao Shen, Odin Zhang, Jike Wang, Jialu Wu, Ruofan Jin, Donghao Zhou, Shicheng Chen, Liwei Liu, Xiaorui Wang, Chang-Yu Hsieh, Guangyong Chen, Peichen Pan, Yu Kang, Ting-Jun Hou
Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency. Briefings in bioinformatics 25 (1) (2024)
Renling Hu, Jintu Zhang, Yu Kang, Zhe Wang, Peichen Pan, Yafeng Deng, Chang-Yu Hsieh, Ting-Jun Hou
Comprehensive, Open-Source, and Automated Workflow for Multisite λ-Dynamics in Lead Optimization. Journal of chemical theory and computation 20 (3) (2024)
Tianyue Wang, Langcheng Wang, Xujun Zhang, Chao Shen, Odin Zhang, Jike Wang, Jialu Wu, Ruofan Jin, Donghao Zhou, Shicheng Chen, Liwei Liu, Xiaorui Wang, Chang-Yu Hsieh, Guangyong Chen, Peichen Pan, Yu Kang, Ting-Jun Hou
Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency. Briefings in bioinformatics 25 (1) (2024)
Mingyang Wang, Zhengjian Wu, Jike Wang, Gaoqi Weng, Yu Kang, Peichen Pan, Dan Li, Yafeng Deng, Xiaojun Yao, Zhitong Bing, Chang-Yu Hsieh, Ting-Jun Hou
Genetic Algorithm-Based Receptor Ligand: A Genetic Algorithm-Guided Generative Model to Boost the Novelty and Drug-Likeness of Molecules in a Sampling Chemical Space. Journal of chemical information and modeling 64 (4) (2024)
Renling Hu, Jintu Zhang, Yu Kang, Zhe Wang, Peichen Pan, Yafeng Deng, Chang-Yu Hsieh, Ting-Jun Hou
Comprehensive, Open-Source, and Automated Workflow for Multisite λ-Dynamics in Lead Optimization. Journal of chemical theory and computation 20 (3) (2024)
Mingyang Wang, Zhengjian Wu, Jike Wang, Gaoqi Weng, Yu Kang, Peichen Pan, Dan Li, Yafeng Deng, Xiaojun Yao, Zhitong Bing, Chang-Yu Hsieh, Ting-Jun Hou
Genetic Algorithm-Based Receptor Ligand: A Genetic Algorithm-Guided Generative Model to Boost the Novelty and Drug-Likeness of Molecules in a Sampling Chemical Space. Journal of chemical information and modeling 64 (4) (2024)
Tianyue Wang, Langcheng Wang, Xujun Zhang, Chao Shen, Odin Zhang, Jike Wang, Jialu Wu, Ruofan Jin, Donghao Zhou, Shicheng Chen, Liwei Liu, Xiaorui Wang, Chang-Yu Hsieh, Guangyong Chen, Peichen Pan, Yu Kang, Ting-Jun Hou
Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency. Briefings in bioinformatics 25 (1) (2024)
Mingyang Wang, Zhengjian Wu, Jike Wang, Gaoqi Weng, Yu Kang, Peichen Pan, Dan Li, Yafeng Deng, Xiaojun Yao, Zhitong Bing, Chang-Yu Hsieh, Ting-Jun Hou
Genetic Algorithm-Based Receptor Ligand: A Genetic Algorithm-Guided Generative Model to Boost the Novelty and Drug-Likeness of Molecules in a Sampling Chemical Space. Journal of chemical information and modeling 64 (4) (2024)
Mingyang Wang, Zhengjian Wu, Jike Wang, Gaoqi Weng, Yu Kang, Peichen Pan, Dan Li, Yafeng Deng, Xiaojun Yao, Zhitong Bing, Chang-Yu Hsieh, Ting-Jun Hou
Genetic Algorithm-Based Receptor Ligand: A Genetic Algorithm-Guided Generative Model to Boost the Novelty and Drug-Likeness of Molecules in a Sampling Chemical Space. Journal of chemical information and modeling (2024)
Renling Hu, Jintu Zhang, Yu Kang, Zhe Wang, Peichen Pan, Yafeng Deng, Chang-Yu Hsieh, Ting-Jun Hou
Comprehensive, Open-Source, and Automated Workflow for Multisite λ-Dynamics in Lead Optimization. Journal of chemical theory and computation (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)
Hongyan Du, Dejun Jiang, Odin Zhang, Zhenxing Wu, Junbo Gao, Xujun Zhang, Xiaorui Wang, Yafeng Deng, Yu Kang, Dan Li, Peichen Pan, Chang-Yu Hsieh, Ting-Jun Hou
A flexible data-free framework for structure-based de novo drug design with reinforcement learning. Chemical science 14 (43) (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)
Haiyang Zhong, Xinyue Wang, Shicheng Chen, Zhe Wang, Huating Wang, Lei Xu, Ting-Jun Hou, Xiao-Jun Yao, Dan Li, Peichen Pan
Discovery of Novel Inhibitors of BRD4 for Treating Prostate Cancer: A Comprehensive Case Study for Considering Water Networks in Virtual Screening and Drug Design. Journal of medicinal chemistry 67 (1) (2023)
Haiyang Zhong, Xinyue Wang, Shicheng Chen, Zhe Wang, Huating Wang, Lei Xu, Ting-Jun Hou, Xiao-Jun Yao, Dan Li, Peichen Pan
Discovery of Novel Inhibitors of BRD4 for Treating Prostate Cancer: A Comprehensive Case Study for Considering Water Networks in Virtual Screening and Drug Design. Journal of medicinal chemistry (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, Chao Shen, Tianyue Wang, Yafeng Deng, Yu Kang, Dan Li, Ting-Jun Hou, Peichen Pan
ML-PLIC: a web platform for characterizing protein-ligand interactions and developing machine learning-based scoring functions. Briefings in bioinformatics 24 (5) (2023)
Haiyang Zhong, Xinyue Wang, Shicheng Chen, Zhe Wang, Huating Wang, Lei Xu, Ting-Jun Hou, Xiao-Jun Yao, Dan Li, Peichen Pan
Discovery of Novel Inhibitors of BRD4 for Treating Prostate Cancer: A Comprehensive Case Study for Considering Water Networks in Virtual Screening and Drug Design. Journal of medicinal chemistry 67 (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)
Zhe Wang, Haiyang Zhong, Jintu Zhang, Peichen Pan, Dong Wang, Huan-Xiang Liu, Xiao-Jun Yao, Ting-Jun Hou, Yu Kang
Small-Molecule Conformer Generators: Evaluation of Traditional Methods and AI Models on High-Quality Data Sets. Journal of chemical information and modeling (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)
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)
Jieyu Jin, Dong Wang, Guqin Shi, Jingxiao Bao, Jike Wang, Haotian Zhang, Peichen Pan, Dan Li, Xiao-Jun Yao, Huan-Xiang Liu, Ting-Jun Hou, Yu Kang
FFLOM: A Flow-Based Autoregressive Model for Fragment-to-Lead Optimization. Journal of medicinal chemistry (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)
Haiyang Zhong, Xinyue Wang, Shicheng Chen, Zhe Wang, Huating Wang, Lei Xu, Ting-Jun Hou, Xiao-Jun Yao, Dan Li, Peichen Pan
Discovery of Novel Inhibitors of BRD4 for Treating Prostate Cancer: A Comprehensive Case Study for Considering Water Networks in Virtual Screening and Drug Design. Journal of medicinal chemistry 67 (1) (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)
Xujun Zhang, Chao Shen, Tianyue Wang, Yu Kang, Dan Li, Peichen Pan, Jike Wang, Gaoang Wang, Yafeng Deng, Lei Xu, Dong-Sheng Cao, Ting-Jun Hou, Zhe Wang
Topology-Based and Conformation-Based Decoys Database: An Unbiased Online Database for Training and Benchmarking Machine-Learning Scoring Functions. Journal of medicinal chemistry (2023)
Chao Shen, Xujun Zhang, Yafeng Deng, Junbo Gao, Dong Wang, Lei Xu, Peichen Pan, Ting-Jun Hou, Yu Kang
Boosting Protein-Ligand Binding Pose Prediction and Virtual Screening Based on Residue-Atom Distance Likelihood Potential and Graph Transformer. Journal of medicinal chemistry 65 (15) (2022)
Hongyan Du, Dejun Jiang, Junbo Gao, Xujun Zhang, Lingxiao Jiang, Yundian Zeng, Zhenxing Wu, Chao Shen, Lei Xu, Dong-Sheng Cao, Ting-Jun Hou, Peichen Pan
Proteome-Wide Profiling of the Covalent-Druggable Cysteines with a Structure-Based Deep Graph Learning Network. Research (Washington, D.C.) 2022 (2022)
Rui Shi, Peichen Pan, Rui Lv, Chongqing Ma, Enhui Wu, Ruochen Guo, Zhihao Zhao, Hexing Song, Joe Zhou, Yang Liu, Guoqiang Xu, Ting-Jun Hou, Zhen-Hui Kang, Jian Liu
High-throughput glycolytic inhibitor discovery targeting glioblastoma by graphite dots-assisted LDI mass spectrometry. Science advances 8 (7) (2022)