Mingyue Zheng

58 papers A* 4C 1Journal 51Unranked 2
YearRankTypeTitle / Venue / Authors
2025 A* conf
Empower Structure-Based Molecule Optimization with Gradient Guided Bayesian Flow Networks.
ICML
Keyue Qiu, Yuxuan Song, Jie Yu, Hongbo Ma, Ziyao Cao, Zhilong Zhang, Yushuai Wu, Mingyue Zheng, Hao Zhou, Wei-Ying Ma
2025 J jnl
Mechanistic Insights into the Allosteric Regulation of P53 Y220C by Small-Molecule Stabilizers.
J. Chem. Inf. Model.
Yiming Wen, Buying Niu, Jingyi Meng, Danye Chen, Xutong Li, Suilin Zhang, Hans Ågren, Mingyue Zheng, Dan Teng
2025 J jnl
MolPIF: A Parameter Interpolation Flow Model for Molecule Generation.
CoRR
Yaowei Jin, Junjie Wang, Wenkai Xiang, Duanhua Cao, Dan Teng, Zhehuan Fan, Jiacheng Xiong, Xia Sheng, Chuanlong Zeng, Duo An, Mingyue Zheng, Shuangjia Zheng, Qian Shi
2025 A* conf
Piloting Structure-Based Drug Design via Modality-Specific Optimal Schedule.
ICML
Keyue Qiu, Yuxuan Song, Zhehuan Fan, Peidong Liu, Zhe Zhang, Mingyue Zheng, Hao Zhou, Wei-Ying Ma
2025 J jnl
Piloting Structure-Based Drug Design via Modality-Specific Optimal Schedule.
CoRR
Keyue Qiu, Yuxuan Song, Zhehuan Fan, Peidong Liu, Zhe Zhang, Mingyue Zheng, Hao Zhou, Wei-Ying Ma
2025 J jnl
miCGR: interpretable deep neural network for predicting both site-level and gene-level functional targets of microRNA.
Briefings Bioinform.
Xiaolong Wu, Lehan Zhang, Xiaochu Tong, Yitian Wang, Zimei Zhang, Xiangtai Kong, Shengkun Ni, Xiaomin Luo, Mingyue Zheng, Yun Tang, Xutong Li
2024 J jnl
FAPM: functional annotation of proteins using multimodal models beyond structural modeling.
Bioinform.
Wenkai Xiang, Zhaoping Xiong, Huan Chen, Jiacheng Xiong, Wei Zhang, Zunyun Fu, Mingyue Zheng, Bing Liu, Qian Shi
2024 J jnl
GENNDTI: Drug-Target Interaction Prediction Using Graph Neural Network Enhanced by Router Nodes.
IEEE J. Biomed. Health Informatics
Beiyuan Yang, Yule Liu, Junfeng Wu, Fang Bai, Mingyue Zheng, Jie Zheng
2024 J jnl
Generic protein-ligand interaction scoring by integrating physical prior knowledge and data augmentation modelling.
Nat. Mac. Intell.
Duanhua Cao, Geng Chen, Jiaxin Jiang, Jie Yu, Runze Zhang, Mingan Chen, Wei Zhang, Lifan Chen, Feisheng Zhong, Yingying Zhang, Chenghao Lu, Xutong Li, Xiaomin Luo, Sulin Zhang, Mingyue Zheng
2024 J jnl
Gram matrix: an efficient representation of molecular conformation and learning objective for molecular pretraining.
Briefings Bioinform.
Wenkai Xiang, Feisheng Zhong, Lin Ni, Mingyue Zheng, Xutong Li, Qian Shi, Dingyan Wang
2024 J jnl
KinomeMETA: meta-learning enhanced kinome-wide polypharmacology profiling.
Briefings Bioinform.
Qun Ren, Ning Qu, Jingjing Sun, Jingyi Zhou, Jin Liu, Lin Ni, Xiaochu Tong, Zimei Zhang, Xiangtai Kong, Yiming Wen, Yitian Wang, Dingyan Wang, Xiaomin Luo, Sulin Zhang, Mingyue Zheng, Xutong Li
2024 A* conf
MolCRAFT: Structure-Based Drug Design in Continuous Parameter Space.
ICML
Yanru Qu, Keyue Qiu, Yuxuan Song, Jingjing Gong, Jiawei Han, Mingyue Zheng, Hao Zhou, Wei-Ying Ma
2024 J jnl
MolCRAFT: Structure-Based Drug Design in Continuous Parameter Space.
CoRR
Yanru Qu, Keyue Qiu, Yuxuan Song, Jingjing Gong, Jiawei Han, Mingyue Zheng, Hao Zhou, Wei-Ying Ma
2024 J jnl
P2DFlow: A Protein Ensemble Generative Model with SE(3) Flow Matching.
CoRR
Yaowei Jin, Qi Huang, Ziyang Song, Mingyue Zheng, Dan Teng, Qian Shi
2024 J jnl
Reducing overconfident errors in molecular property classification using Posterior Network.
Patterns
Zhehuan Fan, Jie Yu, Xiang Zhang, Yijie Chen, Shihui Sun, Yuanyuan Zhang, Mingan Chen, Fu Xiao, Wenyong Wu, Xutong Li, Mingyue Zheng, Xiaomin Luo, Dingyan Wang
2024 J jnl
Structure-Based Drug Design via 3D Molecular Generative Pre-training and Sampling.
CoRR
Yuwei Yang, Siqi Ouyang, Xueyu Hu, Mingyue Zheng, Hao Zhou, Lei Li
2024 J jnl
Structure-Based Molecule Optimization via Gradient-Guided Bayesian Update.
CoRR
Keyue Qiu, Yuxuan Song, Jie Yu, Hongbo Ma, Ziyao Cao, Zhilong Zhang, Yushuai Wu, Mingyue Zheng, Hao Zhou, Wei-Ying Ma
2024 J jnl
TG468: a text graph convolutional network for predicting clinical response to immune checkpoint inhibitor therapy.
Briefings Bioinform.
Kun Wang, Jiangshan Shi, Xiaochu Tong, Ning Qu, Xiangtai Kong, Shengkun Ni, Jing Xing, Xutong Li, Mingyue Zheng
2024 J jnl
Unified Generative Modeling of 3D Molecules via Bayesian Flow Networks.
CoRR
Yuxuan Song, Jingjing Gong, Yanru Qu, Hao Zhou, Mingyue Zheng, Jingjing Liu, Wei-Ying Ma
2024 A* conf
Unified Generative Modeling of 3D Molecules with Bayesian Flow Networks.
ICLR
Yuxuan Song, Jingjing Gong, Hao Zhou, Mingyue Zheng, Jingjing Liu, Wei-Ying Ma
2023 J jnl
An explainable molecular property prediction via multi-granularity.
Inf. Sci.
Haichao Sun, Guoyin Wang, Qun Liu, Jie Yang, Mingyue Zheng
2023 J jnl
Computing the relative binding affinity of ligands based on a pairwise binding comparison network.
Nat. Comput. Sci.
Jie Yu, Zhaojun Li, Geng Chen, Xiangtai Kong, Jie Hu, Dingyan Wang, Duanhua Cao, Yanbei Li, Ruifeng Huo, Gang Wang, Xiaohong Liu, Hualiang Jiang, Xutong Li, Xiaomin Luo, Mingyue Zheng
2023 — conf
Enhancing Temperature Immunity of Digital Circuit Against Aging : The Standard Cell Subset Method.
ASICON
Mingyue Zheng, Wangyong Chen, Yaoyang Lyu, Haifeng Chen, Jiahui Chen, Linlin Cai
2023 J jnl
LogD7.4 prediction enhanced by transferring knowledge from chromatographic retention time, microscopic pKa and logP.
J. Cheminformatics
Yitian Wang, Jiacheng Xiong, Fu Xiao, Wei Zhang, Kaiyang Cheng, Jingxin Rao, Buying Niu, Xiaochu Tong, Ning Qu, Runze Zhang, Dingyan Wang, Kaixian Chen, Xutong Li, Mingyue Zheng
2023 J jnl
MolFilterGAN: a progressively augmented generative adversarial network for triaging AI-designed molecules.
J. Cheminformatics
Xiaohong Liu, Wei Zhang, Xiaochu Tong, Feisheng Zhong, Zhaojun Li, Zhaoping Xiong, Jiacheng Xiong, Xiaolong Wu, Zunyun Fu, Xiaoqin Tan, Zhiguo Liu, Sulin Zhang, Hualiang Jiang, Xutong Li, Mingyue Zheng
2023 J jnl
RNAincoder: a deep learning-based encoder for RNA and RNA-associated interaction.
Nucleic Acids Res.
Yunxia Wang, Zhen Chen, Ziqi Pan, Shijie Huang, Jin Liu, Weiqi Xia, Hongning Zhang, Mingyue Zheng, Honglin Li, Tingjun Hou, Feng Zhu
2023 J jnl
Tora3D: an autoregressive torsion angle prediction model for molecular 3D conformation generation.
J. Cheminformatics
Zimei Zhang, Gang Wang, Rui Li, Lin Ni, Runze Zhang, Kaiyang Cheng, Qun Ren, Xiangtai Kong, Shengkun Ni, Xiaochu Tong, Li Luo, Dingyan Wang, Xiaojie Lu, Mingyue Zheng, Xutong Li
2022 J jnl
An inductive graph neural network model for compound-protein interaction prediction based on a homogeneous graph.
Briefings Bioinform.
Xiaozhe Wan, Xiaolong Wu, Dingyan Wang, Xiaoqin Tan, Xiaohong Liu, Zunyun Fu, Hualiang Jiang, Mingyue Zheng, Xutong Li
2022 J jnl
Blood-brain barrier penetration prediction enhanced by uncertainty estimation.
J. Cheminformatics
Xiaochu Tong, Dingyan Wang, Xiaoyu Ding, Xiaoqin Tan, Qun Ren, Geng Chen, Yu Rong, Tingyang Xu, Junzhou Huang, Hualiang Jiang, Mingyue Zheng, Xutong Li
2022 J jnl
Multi-instance learning of graph neural networks for aqueous pKa prediction.
Bioinform.
Jiacheng Xiong, Zhaojun Li, Guangchao Wang, Zunyun Fu, Feisheng Zhong, Tingyang Xu, Xiaomeng Liu, Ziming Huang, Xiaohong Liu, Kaixian Chen, Hualiang Jiang, Mingyue Zheng
2022 C conf
Popular Music Production Trend Analysis and Prediction Research.
CHIRA
Mingyue Zheng, Jiarui Jin
2021 J jnl
A hybrid framework for improving uncertainty quantification in deep learning-based QSAR regression modeling.
J. Cheminformatics
Dingyan Wang, Jie Yu, Lifan Chen, Xutong Li, Hualiang Jiang, Kaixian Chen, Mingyue Zheng, Xiaomin Luo
2021 J jnl
Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge.
PLoS Comput. Biol.
Zhaoping Xiong, Minji Jeon, Robert J. Allaway, Jaewoo Kang, Donghyeon Park, Jinhyuk Lee, Hwisang Jeon, Miyoung Ko, Hualiang Jiang, Mingyue Zheng, Aik Choon Tan, Xindi Guo, Multi-Targeting Drug DREAM Challenge Community, Kristen K. Dang, Alexander Tropsha, Chana Hecht, Tirtha K. Das, Heather A. Carlson, Ruben Abagyan, Justin Guinney, Avner Schlessinger, Ross L. Cagan
2021 J jnl
Drug repurposing against breast cancer by integrating drug-exposure expression profiles and drug-drug links based on graph neural network.
Bioinform.
Chen Cui, Xiaoyu Ding, Dingyan Wang, Lifan Chen, Fu Xiao, Tingyang Xu, Mingyue Zheng, Xiaomin Luo, Hualiang Jiang, Kaixian Chen
2021 J jnl
DrugSpaceX: a large screenable and synthetically tractable database extending drug space.
Nucleic Acids Res.
Tianbiao Yang, Zhaojun Li, Yingjia Chen, Dan Feng, Guangchao Wang, Zunyun Fu, Xiaoyu Ding, Xiaoqin Tan, Jihui Zhao, Xiaomin Luo, Kaixian Chen, Hualiang Jiang, Mingyue Zheng
2020 — conf
A Realization Framework of International Image Prediction System for Film and TV Works.
CISP-BMEI
Shan Liu, Xiaoqing Wu, Mingyue Zheng, Xinqiao Cheng, Ruijing Fang, Pingru Long
2020 J jnl
TransformerCPI: improving compound-protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments.
Bioinform.
Lifan Chen, Xiaoqin Tan, Dingyan Wang, Feisheng Zhong, Xiaohong Liu, Tianbiao Yang, Xiaomin Luo, Kaixian Chen, Hualiang Jiang, Mingyue Zheng, Arne Elofsson
2019 J jnl
KinomeX: a web application for predicting kinome-wide polypharmacology effect of small molecules.
Bioinform.
Zhaojun Li, Xutong Li, Xiaohong Liu, Zunyun Fu, Zhaoping Xiong, Xiaolong Wu, Xiaoqin Tan, Jihui Zhao, Feisheng Zhong, Xiaozhe Wan, Xiaomin Luo, Kaixian Chen, Hualiang Jiang, Mingyue Zheng
2017 J jnl
Machine-Learning-Assisted Approach for Discovering Novel Inhibitors Targeting Bromodomain-Containing Protein 4.
J. Chem. Inf. Model.
Jing Xing, Wenchao Lu, Rongfeng Liu, Yulan Wang, Yiqian Xie, Hao Zhang, Zhe Shi, Hao Jiang, Yu-Chih Liu, Kaixian Chen, Hualiang Jiang, Cheng Luo, Mingyue Zheng
2016 J jnl
Discovery of Novel Inhibitors Targeting the Menin-Mixed Lineage Leukemia Interface Using Pharmacophore- and Docking-Based Virtual Screening.
J. Chem. Inf. Model.
Yuan Xu, Liyan Yue, Yulan Wang, Jing Xing, Zhifeng Chen, Zhe Shi, Rongfeng Liu, Yu-Chih Liu, Xiaomin Luo, Hualiang Jiang, Kaixian Chen, Cheng Luo, Mingyue Zheng
2016 J jnl
Identification of Novel Disruptor of Telomeric Silencing 1-like (DOT1L) Inhibitors through Structure-Based Virtual Screening and Biological Assays.
J. Chem. Inf. Model.
Shijie Chen, Linjuan Li, Yantao Chen, Junchi Hu, Jingqiu Liu, Yu-Chih Liu, Rongfeng Liu, Yuanyuan Zhang, Fanwang Meng, Kongkai Zhu, Junyan Lu, Mingyue Zheng, Kaixian Chen, Jin Zhang, Hualiang Jiang, Zhiyi Yao, Cheng Luo
2015 J jnl
TarPred: a web application for predicting therapeutic and side effect targets of chemical compounds.
Bioinform.
Xian Liu, Yuan Gao, Jianlong Peng, Yuan Xu, Yulan Wang, Nannan Zhou, Jing Xing, Xiaomin Luo, Hualiang Jiang, Mingyue Zheng
2014 J jnl
Estimation of acute oral toxicity in rat using local lazy learning.
J. Cheminformatics
Jing Lu, Jianlong Peng, Jinan Wang, Qiancheng Shen, Yi Bi, Likun Gong, Mingyue Zheng, Xiaomin Luo, Weiliang Zhu, Hualiang Jiang, Kaixian Chen
2014 J jnl
In Silico target fishing: addressing a "Big Data" problem by ligand-based similarity rankings with data fusion.
J. Cheminformatics
Xian Liu, Yuan Xu, Shanshan Li, Yulan Wang, Jianlong Peng, Cheng Luo, Xiaomin Luo, Mingyue Zheng, Kaixian Chen, Hualiang Jiang
2013 J jnl
A quantum mechanics/molecular mechanics study on the hydrolysis mechanism of New Delhi metallo-β-lactamase-1.
J. Comput. Aided Mol. Des.
Kongkai Zhu, Junyan Lu, Zhongjie Liang, Xiangqian Kong, Fei Ye, Lu Jin, Heji Geng, Yong Chen, Mingyue Zheng, Hualiang Jiang, Jun-Qian Li, Cheng Luo
2013 J jnl
Water PMF for predicting the properties of water molecules in protein binding site.
J. Comput. Chem.
Mingyue Zheng, Yanlian Li, Bing Xiong, Hualiang Jiang, Jingkang Shen
2012 J jnl
Estimation of Carcinogenicity Using Molecular Fragments Tree.
J. Chem. Inf. Model.
Yong Wang, Jing Lu, Fei Wang, Qiancheng Shen, Mingyue Zheng, Xiaomin Luo, Weiliang Zhu, Hualiang Jiang, Kaixian Chen
2012 J jnl
Unbinding Pathways of GW4064 from Human Farnesoid X Receptor As Revealed by Molecular Dynamics Simulations.
J. Chem. Inf. Model.
Weihua Li, Jing Fu, Feixiong Cheng, Mingyue Zheng, Jian Zhang, Guixia Liu, Yun Tang
2011 J jnl
Computational Screening for Active Compounds Targeting Protein Sequences: Methodology and Experimental Validation.
J. Chem. Inf. Model.
Fei Wang, Dongxiang Liu, Heyao Wang, Cheng Luo, Mingyue Zheng, Hong Liu, Weiliang Zhu, Xiaomin Luo, Jian Zhang, Hualiang Jiang
2011 J jnl
Fragment-based prediction of skin sensitization using recursive partitioning.
J. Comput. Aided Mol. Des.
Jing Lu, Mingyue Zheng, Yong Wang, Qiancheng Shen, Xiaomin Luo, Hualiang Jiang, Kaixian Chen
2011 J jnl
Knowledge-Based Scoring Functions in Drug Design: 2. Can the Knowledge Base Be Enriched?
J. Chem. Inf. Model.
Qiancheng Shen, Bing Xiong, Mingyue Zheng, Xiaomin Luo, Cheng Luo, Xian Liu, Yun Du, Jing Li, Weiliang Zhu, Jingkang Shen, Hualiang Jiang
2011 J jnl
Knowledge-Based Scoring Functions in Drug Design: 3. A Two-Dimensional Knowledge-Based Hydrogen-Bonding Potential for the Prediction of Protein-Ligand Interactions.
J. Chem. Inf. Model.
Mingyue Zheng, Bing Xiong, Cheng Luo, Shanshan Li, Xian Liu, Qiancheng Shen, Jing Li, Weiliang Zhu, Xiaomin Luo, Hualiang Jiang
2010 J jnl
Knowledge-Based Scoring Functions in Drug Design. 1. Developing a Target-Specific Method for Kinase-Ligand Interactions.
J. Chem. Inf. Model.
Mengzhu Xue, Mingyue Zheng, Bing Xiong, Yanlian Li, Hualiang Jiang, Jingkang Shen
2009 J jnl
An effective docking strategy for virtual screening based on multi-objective optimization algorithm.
BMC Bioinform.
Honglin Li, Hailei Zhang, Mingyue Zheng, Jie Luo, Ling Kang, Xiaofeng Liu, Xicheng Wang, Hualiang Jiang
2009 J jnl
Site of metabolism prediction for six biotransformations mediated by cytochromes P450.
Bioinform.
Mingyue Zheng, Xiaomin Luo, Qiancheng Shen, Yong Wang, Yun Du, Weiliang Zhu, Hualiang Jiang
2006 J jnl
Mutagenic probability estimation of chemical compounds by a novel molecular electrophilicity vector and support vector machine.
Bioinform.
Mingyue Zheng, Zhiguo Liu, Chunxia Xue, Weiliang Zhu, Kaixian Chen, Xiaomin Luo, Hualiang Jiang
2006 J jnl
QSAR analyses on avian influenza virus neuraminidase inhibitors using CoMFA, CoMSIA, and HQSAR.
J. Comput. Aided Mol. Des.
Mingyue Zheng, Kunqian Yu, Hong Liu, Xiaomin Luo, Kaixian Chen, Weiliang Zhu, Hualiang Jiang
2006 J jnl
Towards discovering dual functional inhibitors against both wild type and K103N mutant HIV-1 reverse transcriptases: molecular docking and QSAR studies on 4, 1-benzoxazepinone analogues.
J. Comput. Aided Mol. Des.
Zhenshan Zhang, Mingyue Zheng, Li Du, Jianhua Shen, Xiaomin Luo, Weiliang Zhu, Hualiang Jiang