A New Approach to Design Virtual Combinatorial Library with Genetic Algorithm Based on 3D Grid Property. - DongXiang Liu; Hualiang Jiang; Kaixian Chen; RuYun Ji (J. Chem. Inf. Comput. Sci., 1998)

A New Rapid and Effective Chemistry Space Filter in Recognizing a Druglike Database. - Suxin Zheng; Xiaomin Luo; Gang Chen; Weiliang Zhu; Jianhua Shen; Kaixian Chen; Hualiang Jiang (J. Chem. Inf. Model., 2005)

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)

TarFisDock: a web server for identifying drug targets with docking approach. - Honglin Li 003; Zhenting Gao; Ling Kang; Hailei Zhang; Kun Yang; Kunqian Yu; Xiaomin Luo; Weiliang Zhu; Kaixian Chen; Jianhua Shen; Xicheng Wang; Hualiang Jiang (Nucleic Acids Res., 2006)

Why does beta-secretase zymogen possess catalytic activity? Molecular modeling and molecular dynamics simulation studies. - Zhili Zuo; Chen Gang; Hanjun Zou; Puah Chum Mok; Weiliang Zhu; Kaixian Chen; Hualiang Jiang (Comput. Biol. Chem., 2007)

DDGrid: A Grid Computing Environment with Massive Concurrency and Fault-Tolerance Support. - Yongjian Wang; Zhongzhi Luan; Depei Qian; Yuanqiang Huang; Ting Chen; Biao Han; Yinan Ren; Kunqian Yu; Hualiang Jiang (GCC, 2008)

DrugViz: a Cytoscape plugin for visualizing and analyzing small molecule drugs in biological networks. - Bing Xiong 003; Ke Liu; Jie Wu; David L. Burk; Hualiang Jiang; Jingkang Shen (Bioinform., 2008)

PDTD: a web-accessible protein database for drug target identification. - Zhenting Gao; Honglin Li 003; Hailei Zhang; Xiaofeng Liu 005; Ling Kang; Xiaomin Luo; Weiliang Zhu; Kaixian Chen; Xicheng Wang; Hualiang Jiang (BMC Bioinform., 2008)

An Improved PMF Scoring Function for Universally Predicting the Interactions of a Ligand with Protein, DNA, and RNA. - Xiaoyu Zhao; Xiaofeng Liu 005; Yuanyuan Wang; Zhi Chen; Ling Kang; Hailei Zhang; Xiaomin Luo; Weiliang Zhu; Kaixian Chen; Honglin Li 003; Xicheng Wang; Hualiang Jiang (J. Chem. Inf. Model., 2008)

Mechanics of Channel Gating of the Nicotinic Acetylcholine Receptor. - Xinli Liu; Yechun Xu; Honglin Li 003; Xicheng Wang; Hualiang Jiang; Francisco J. Barrantes (PLoS Comput. Biol., 2008)

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)

Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation. - Xiaofeng Liu 005; Fang Bai; Sisheng Ouyang; Xicheng Wang; Honglin Li 003; Hualiang Jiang (BMC Bioinform., 2009)

An improved adaptive genetic algorithm for protein-ligand docking. - Ling Kang; Honglin Li 003; Hualiang Jiang; Xicheng Wang (J. Comput. Aided Mol. Des., 2009)

Optimizing Energy Potential for Protein Fold Recognition with Parametric Evaluation Function. - Junfeng Gu; Honglin Li 003; Hualiang Jiang; Xicheng Wang (J. Comput. Biol., 2009)

Bioactive Conformational Generation of Small Molecules: A Comparative Analysis between Force-Field and Multiple Empirical Criteria Based Methods. - Fang Bai; Xiaofeng Liu 005; Jiabo Li; Haoyun Zhang; Hualiang Jiang; Xicheng Wang; Honglin Li 003 (BMC Bioinform., 2010)

BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server. - Bing Xiong 003; Jie Wu; David L. Burk; Mengzhu Xue; Hualiang Jiang; Jingkang Shen (BMC Bioinform., 2010)

Multiple Pharmacophore Models Combined with Molecular Docking: A Reliable Way for Efficiently Identifying Novel PDE4 Inhibitors with High Structural Diversity. - Zhi Chen; Guanghui Tian; Zhen Wang; Hualiang Jiang; Jingshan Shen; Weiliang Zhu (J. Chem. Inf. Model., 2010)

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)

PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach. - Xiaofeng Liu 005; Sisheng Ouyang; Biao Yu; Yabo Liu; Kai Huang; Jiayu Gong; Siyuan Zheng; Zhihua Li; Honglin Li 003; Hualiang Jiang (Nucleic Acids Res., 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)

SHAFTS: A Hybrid Approach for 3D Molecular Similarity Calculation. 1. Method and Assessment of Virtual Screening. - Xiaofeng Liu 005; Hualiang Jiang; Honglin Li 003 (J. Chem. Inf. Model., 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)

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)

ChemMapper: a versatile web server for exploring pharmacology and chemical structure association based on molecular 3D similarity method. - Jiayu Gong; Chaoqian Cai; Xiaofeng Liu 005; Xin Ku; Hualiang Jiang; Daqi Gao; Honglin Li 003 (Bioinform., 2013)

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)

Discovery of Novel Acetohydroxyacid Synthase Inhibitors as Active Agents against Mycobacterium tuberculosis by Virtual Screening and Bioassay. - Di Wang; Xuelian Zhu; Changjun Cui; Mei Dong; Hualiang Jiang; Zhengming Li; Zhen Liu; Weiliang Zhu; Jianguo Wang (J. Chem. Inf. Model., 2013)

Molecular Modeling of the 3D Structure of 5-HT1AR: Discovery of Novel 5-HT1AR Agonists via Dynamic Pharmacophore-Based Virtual Screening. - Lili Xu; Shanglin Zhou; Kunqian Yu; Bo Gao; Hualiang Jiang; Xuechu Zhen; Wei Fu (J. Chem. Inf. Model., 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)

iDrug: a web-accessible and interactive drug discovery and design platform. - Xia Wang; Haipeng Chen; Feng Yang; Jiayu Gong; Shiliang Li; Jianfeng Pei; Xiaofeng Liu 005; Hualiang Jiang; Luhua Lai; Honglin Li 003 (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)

An Accurate Metalloprotein-Specific Scoring Function and Molecular Docking Program Devised by a Dynamic Sampling and Iteration Optimization Strategy. - Fang Bai; Sha Liao; Junfeng Gu; Hualiang Jiang; Xicheng Wang; Honglin Li 003 (J. Chem. Inf. Model., 2015)

Molecular Mechanism underlying PRMT1 Dimerization for SAM Binding and Methylase Activity. - Ran Zhou; Yiqian Xie; Hao Hu; Guang Hu 001; Viral Sanjay Patel; Jin Zhang; Kunqian Yu; Yiran Huang; Hualiang Jiang; Zhongjie Liang; Yujun George Zheng; Cheng Luo (J. Chem. Inf. Model., 2015)

Understanding Voltage Gating of Providencia stuartii Porins at Atomic Level. - Wanling Song; Harsha Bajaj; Chady Nasrallah; Hualiang Jiang; Mathias Winterhalter; Jacques-Philippe Colletier; Yechun Xu (PLoS Comput. Biol., 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)

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)

MA-GAN: A Method Based on Generative Adversarial Network for Calligraphy Morphing. - Jiaxin Zhao; Yang Zhang; Xiaohu Ma; Dongdong Yang; Yao Shen; Hualiang Jiang (ICONIP (1), 2021)

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)

Image Inpainting Based Multi-scale Gated Convolution and Attention. - Hualiang Jiang; Xiaohu Ma; Dongdong Yang; Jiaxin Zhao; Yao Shen (ICANN (2), 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)

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)

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)

Loops Mediate Agonist-Induced Activation of the Stimulator of Interferon Genes Protein. - Rui Li; Lin Chen; Xinheng He; Duanhua Cao; Zehong Zhang; Hualiang Jiang; Kaixian Chen; Xi Cheng (J. Chem. Inf. Model., 2023)