Mutagenic probability estimation of chemical compounds by a novel molecular electrophilicity vector and support vector machine. - Mingyue Zheng; Zhiguo Liu; Chunxia Xue; Weiliang Zhu; Kaixian Chen; Xiaomin Luo; Hualiang Jiang (Bioinform., 2006)

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. - Zhenshan Zhang; Mingyue Zheng; Li Du; Jianhua Shen; Xiaomin Luo; Weiliang Zhu; Hualiang Jiang (J. Comput. Aided Mol. Des., 2006)

QSAR analyses on avian influenza virus neuraminidase inhibitors using CoMFA, CoMSIA, and HQSAR. - Mingyue Zheng; Kunqian Yu; Hong Liu; Xiaomin Luo; Kaixian Chen; Weiliang Zhu; Hualiang Jiang (J. Comput. Aided Mol. Des., 2006)

Site of metabolism prediction for six biotransformations mediated by cytochromes P450. - Mingyue Zheng; Xiaomin Luo; Qiancheng Shen; Yong Wang; Yun Du; Weiliang Zhu; Hualiang Jiang (Bioinform., 2009)

An effective docking strategy for virtual screening based on multi-objective optimization algorithm. - Honglin Li 003; Hailei Zhang; Mingyue Zheng; Jie Luo; Ling Kang; Xiaofeng Liu 005; Xicheng Wang; Hualiang Jiang (BMC Bioinform., 2009)

Knowledge-Based Scoring Functions in Drug Design. 1. Developing a Target-Specific Method for Kinase-Ligand Interactions. - Mengzhu Xue; Mingyue Zheng; Bing Xiong 003; Yanlian Li; Hualiang Jiang; Jingkang Shen (J. Chem. Inf. Model., 2010)

Fragment-based prediction of skin sensitization using recursive partitioning. - Jing Lu; Mingyue Zheng; Yong Wang; Qiancheng Shen; Xiaomin Luo; Hualiang Jiang; Kaixian Chen (J. Comput. Aided Mol. Des., 2011)

Knowledge-Based Scoring Functions in Drug Design: 2. Can the Knowledge Base Be Enriched? - Qiancheng Shen; Bing Xiong 003; Mingyue Zheng; Xiaomin Luo; Cheng Luo; Xian Liu; Yun Du; Jing Li; Weiliang Zhu; Jingkang Shen; Hualiang Jiang (J. Chem. Inf. Model., 2011)

Computational Screening for Active Compounds Targeting Protein Sequences: Methodology and Experimental Validation. - Fei Wang 012; DongXiang Liu; Heyao Wang; Cheng Luo; Mingyue Zheng; Hong Liu; Weiliang Zhu; Xiaomin Luo; Jian Zhang 037; Hualiang Jiang (J. Chem. Inf. Model., 2011)

Knowledge-Based Scoring Functions in Drug Design: 3. A Two-Dimensional Knowledge-Based Hydrogen-Bonding Potential for the Prediction of Protein-Ligand Interactions. - Mingyue Zheng; Bing Xiong 003; Cheng Luo; Shanshan Li; Xian Liu; Qiancheng Shen; Jing Li; Weiliang Zhu; Xiaomin Luo; Hualiang Jiang (J. Chem. Inf. Model., 2011)

Unbinding Pathways of GW4064 from Human Farnesoid X Receptor As Revealed by Molecular Dynamics Simulations. - Weihua Li 005; Jing Fu; Feixiong Cheng; Mingyue Zheng; Jian Zhang 037; Guixia Liu; Yun Tang 001 (J. Chem. Inf. Model., 2012)

Estimation of Carcinogenicity Using Molecular Fragments Tree. - Yong Wang; Jing Lu; Fei Wang 012; Qiancheng Shen; Mingyue Zheng; Xiaomin Luo; Weiliang Zhu; Hualiang Jiang; Kaixian Chen (J. Chem. Inf. Model., 2012)

A quantum mechanics/molecular mechanics study on the hydrolysis mechanism of New Delhi metallo-β-lactamase-1. - 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 (J. Comput. Aided Mol. Des., 2013)

Water PMF for predicting the properties of water molecules in protein binding site. - Mingyue Zheng; Yanlian Li; Bing Xiong 003; Hualiang Jiang; Jingkang Shen (J. Comput. Chem., 2013)

In silico site of metabolism prediction for human UGT-catalyzed reactions. - Jianlong Peng; Jing Lu; Qiancheng Shen; Mingyue Zheng; Xiaomin Luo; Weiliang Zhu; Hualiang Jiang; Kaixian Chen (Bioinform., 2014)

In Silico target fishing: addressing a "Big Data" problem by ligand-based similarity rankings with data fusion. - Xian Liu; Yuan Xu; Shanshan Li; Yulan Wang; Jianlong Peng; Cheng Luo; Xiaomin Luo; Mingyue Zheng; Kaixian Chen; Hualiang Jiang (J. Cheminformatics, 2014)

Estimation of acute oral toxicity in rat using local lazy learning. - Jing Lu; Jianlong Peng; Jinan Wang; Qiancheng Shen; Yi Bi; Likun Gong; Mingyue Zheng; Xiaomin Luo; Weiliang Zhu; Hualiang Jiang; Kaixian Chen (J. Cheminformatics, 2014)

TarPred: a web application for predicting therapeutic and side effect targets of chemical compounds. - Xian Liu; Yuan Gao; Jianlong Peng; Yuan Xu; Yulan Wang; Nannan Zhou; Jing Xing; Xiaomin Luo; Hualiang Jiang; Mingyue Zheng (Bioinform., 2015)

Identification of Novel Disruptor of Telomeric Silencing 1-like (DOT1L) Inhibitors through Structure-Based Virtual Screening and Biological Assays. - 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; et al. (J. Chem. Inf. Model., 2016)

Discovery of Novel Inhibitors Targeting the Menin-Mixed Lineage Leukemia Interface Using Pharmacophore- and Docking-Based Virtual Screening. - 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; et al. (J. Chem. Inf. Model., 2016)

Machine-Learning-Assisted Approach for Discovering Novel Inhibitors Targeting Bromodomain-Containing Protein 4. - 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; et al. (J. Chem. Inf. Model., 2017)

KinomeX: a web application for predicting kinome-wide polypharmacology effect of small molecules. - Zhaojun Li; Xutong Li; Xiaohong Liu 002; Zunyun Fu; Zhaoping Xiong; Xiaolong Wu; Xiaoqin Tan; Jihui Zhao; Feisheng Zhong; Xiaozhe Wan; Xiaomin Luo; Kaixian Chen; et al. (Bioinform., 2019)

A Realization Framework of International Image Prediction System for Film and TV Works. - Shan Liu 003; Xiaoqing Wu; Mingyue Zheng; Xinqiao Cheng; Ruijing Fang; Pingru Long (CISP-BMEI, 2020)

TransformerCPI: improving compound-protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments. - Lifan Chen; Xiaoqin Tan; Dingyan Wang; Feisheng Zhong; Xiaohong Liu 002; Tianbiao Yang; Xiaomin Luo; Kaixian Chen; Hualiang Jiang; Mingyue Zheng; Arne Elofsson (Bioinform., 2020)

Drug repurposing against breast cancer by integrating drug-exposure expression profiles and drug-drug links based on graph neural network. - Chen Cui; Xiaoyu Ding; Dingyan Wang; Lifan Chen; Fu Xiao; Tingyang Xu; Mingyue Zheng; Xiaomin Luo; Hualiang Jiang; Kaixian Chen (Bioinform., 2021)

A hybrid framework for improving uncertainty quantification in deep learning-based QSAR regression modeling. - Dingyan Wang; Jie Yu; Lifan Chen; Xutong Li; Hualiang Jiang; Kaixian Chen; Mingyue Zheng; Xiaomin Luo (J. Cheminformatics, 2021)

DrugSpaceX: a large screenable and synthetically tractable database extending drug space. - Tianbiao Yang; Zhaojun Li; Yingjia Chen; Dan Feng; Guangchao Wang; Zunyun Fu; Xiaoyu Ding; Xiaoqin Tan; Jihui Zhao; Xiaomin Luo; Kaixian Chen; Hualiang Jiang; et al. (Nucleic Acids Res., 2021)

Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge. - 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; et al. (PLoS Comput. Biol., 2021)

Popular Music Production Trend Analysis and Prediction Research. - Mingyue Zheng; Jiarui Jin (CHIRA, 2022)

An inductive graph neural network model for compound-protein interaction prediction based on a homogeneous graph. - Xiaozhe Wan; Xiaolong Wu; Dingyan Wang; Xiaoqin Tan; Xiaohong Liu 002; Zunyun Fu; Hualiang Jiang; Mingyue Zheng; Xutong Li (Briefings Bioinform., 2022)

Multi-instance learning of graph neural networks for aqueous pKa prediction. - Jiacheng Xiong; Zhaojun Li; Guangchao Wang; Zunyun Fu; Feisheng Zhong; Tingyang Xu; Xiaomeng Liu; Ziming Huang; Xiaohong Liu 002; Kaixian Chen; Hualiang Jiang; Mingyue Zheng (Bioinform., 2022)

Blood-brain barrier penetration prediction enhanced by uncertainty estimation. - Xiaochu Tong; Dingyan Wang; Xiaoyu Ding; Xiaoqin Tan; Qun Ren; Geng Chen; Yu Rong 001; Tingyang Xu; Junzhou Huang; Hualiang Jiang; Mingyue Zheng; Xutong Li (J. Cheminformatics, 2022)

Enhancing Temperature Immunity of Digital Circuit Against Aging : The Standard Cell Subset Method. - Mingyue Zheng; Wangyong Chen; Yaoyang Lyu; Haifeng Chen; Jiahui Chen; Linlin Cai (ASICON, 2023)

An explainable molecular property prediction via multi-granularity. - Haichao Sun; Guoyin Wang 001; Qun Liu 005; Jie Yang 052; Mingyue Zheng (Inf. Sci., 2023)

Computing the relative binding affinity of ligands based on a pairwise binding comparison network. - Jie Yu; Zhaojun Li; Geng Chen; Xiangtai Kong; Jie Hu; Dingyan Wang; Duanhua Cao; Yanbei Li; Ruifeng Huo; Gang Wang; Xiaohong Liu 002; Hualiang Jiang; et al. (Nat. Comput. Sci., 2023)

RNAincoder: a deep learning-based encoder for RNA and RNA-associated interaction. - Yunxia Wang; Zhen Chen; Ziqi Pan; Shijie Huang; Jin Liu; Weiqi Xia; Hongning Zhang; Mingyue Zheng; Honglin Li 003; Tingjun Hou; Feng Zhu 004 (Nucleic Acids Res., 2023)

MolFilterGAN: a progressively augmented generative adversarial network for triaging AI-designed molecules. - Xiaohong Liu 002; Wei Zhang; Xiaochu Tong; Feisheng Zhong; Zhaojun Li; Zhaoping Xiong; Jiacheng Xiong; Xiaolong Wu; Zunyun Fu; Xiaoqin Tan; Zhiguo Liu; Sulin Zhang; et al. (J. Cheminformatics, 2023)

LogD7.4 prediction enhanced by transferring knowledge from chromatographic retention time, microscopic pKa and logP. - Yitian Wang; Jiacheng Xiong; Fu Xiao; Wei Zhang; Kaiyang Cheng; Jingxin Rao; Buying Niu; Xiaochu Tong; Ning Qu; Runze Zhang; Dingyan Wang; Kaixian Chen; et al. (J. Cheminformatics, 2023)

Tora3D: an autoregressive torsion angle prediction model for molecular 3D conformation generation. - Zimei Zhang; Gang Wang; Rui Li; Lin Ni; Runze Zhang; Kaiyang Cheng; Qun Ren; Xiangtai Kong; Shengkun Ni; Xiaochu Tong; Li Luo; Dingyan Wang; et al. (J. Cheminformatics, 2023)

Unified Generative Modeling of 3D Molecules with Bayesian Flow Networks. - Yuxuan Song; Jingjing Gong; Hao Zhou 012; Mingyue Zheng; Jingjing Liu; Wei-Ying Ma (ICLR, 2024)

MolCRAFT: Structure-Based Drug Design in Continuous Parameter Space. - Yanru Qu; Keyue Qiu; Yuxuan Song; Jingjing Gong; Jiawei Han 001; Mingyue Zheng; Hao Zhou 012; Wei-Ying Ma (ICML, 2024)

KinomeMETA: meta-learning enhanced kinome-wide polypharmacology profiling. - Qun Ren; Ning Qu; Jingjing Sun; Jingyi Zhou; Jin Liu; Lin Ni; Xiaochu Tong; Zimei Zhang; Xiangtai Kong; Yiming Wen; Yitian Wang; Dingyan Wang; et al. (Briefings Bioinform., 2024)

TG468: a text graph convolutional network for predicting clinical response to immune checkpoint inhibitor therapy. - Kun Wang; Jiangshan Shi; Xiaochu Tong; Ning Qu; Xiangtai Kong; Shengkun Ni; Jing Xing; Xutong Li; Mingyue Zheng (Briefings Bioinform., 2024)

miCGR: interpretable deep neural network for predicting both site-level and gene-level functional targets of microRNA. - Xiaolong Wu; Lehan Zhang; Xiaochu Tong; Yitian Wang; Zimei Zhang; Xiangtai Kong; Shengkun Ni; Xiaomin Luo; Mingyue Zheng; Yun Tang 001; Xutong Li (Briefings Bioinform., 2024)

Gram matrix: an efficient representation of molecular conformation and learning objective for molecular pretraining. - Wenkai Xiang; Feisheng Zhong; Lin Ni; Mingyue Zheng; Xutong Li; Qian Shi 005; Dingyan Wang (Briefings Bioinform., 2024)

Structure-Based Drug Design via 3D Molecular Generative Pre-training and Sampling. - Yuwei Yang; Siqi Ouyang; Xueyu Hu; Mingyue Zheng; Hao Zhou 012; Lei Li 005 (CoRR, 2024)

Unified Generative Modeling of 3D Molecules via Bayesian Flow Networks. - Yuxuan Song; Jingjing Gong; Yanru Qu; Hao Zhou 012; Mingyue Zheng; Jingjing Liu; Wei-Ying Ma (CoRR, 2024)

Structure-Based Molecule Optimization via Gradient-Guided Bayesian Update. - Keyue Qiu; Yuxuan Song; Jie Yu; Hongbo Ma; Ziyao Cao; Zhilong Zhang; Yushuai Wu; Mingyue Zheng; Hao Zhou 012; Wei-Ying Ma (CoRR, 2024)

P2DFlow: A Protein Ensemble Generative Model with SE(3) Flow Matching. - Yaowei Jin; Qi Huang; Ziyang Song; Mingyue Zheng; Dan Teng; Qian Shi 005 (CoRR, 2024)

Generic protein-ligand interaction scoring by integrating physical prior knowledge and data augmentation modelling. - Duanhua Cao; Geng Chen; Jiaxin Jiang; Jie Yu; Runze Zhang; Mingan Chen; Wei Zhang; Lifan Chen; Feisheng Zhong; Yingying Zhang; Chenghao Lu; Xutong Li; et al. (Nat. Mac. Intell., 2024)

Reducing overconfident errors in molecular property classification using Posterior Network. - Zhehuan Fan; Jie Yu; Xiang Zhang; Yijie Chen; Shihui Sun; Yuanyuan Zhang; Mingan Chen; Fu Xiao; Wenyong Wu; Xutong Li; Mingyue Zheng; Xiaomin Luo; et al. (Patterns, 2024)

GENNDTI: Drug-Target Interaction Prediction Using Graph Neural Network Enhanced by Router Nodes. - Beiyuan Yang; Yule Liu; Junfeng Wu; Fang Bai; Mingyue Zheng; Jie Zheng 002 (IEEE J. Biomed. Health Informatics, 2024)

Piloting Structure-Based Drug Design via Modality-Specific Optimal Schedule. - Keyue Qiu; Yuxuan Song; Zhehuan Fan; Peidong Liu; Zhe Zhang; Mingyue Zheng; Hao Zhou 012; Wei-Ying Ma (CoRR, 2025)

MolPIF: A Parameter Interpolation Flow Model for Molecule Generation. - Yaowei Jin; Junjie Wang; Wenkai Xiang; Duanhua Cao; Dan Teng; Zhehuan Fan; Jiacheng Xiong; Xia Sheng; Chuanlong Zeng; Duo An; Mingyue Zheng; Shuangjia Zheng; et al. (CoRR, 2025)