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)

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)

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)

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: 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)

A computational analysis of binding modes and conformation changes of MDM2 induced by p53 and inhibitor bindings. - Jianzhong Chen; Jinan Wang; Weiliang Zhu; Guohui Li (J. Comput. Aided Mol. Des., 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)

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)

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)

Halogen Bond: Its Role beyond Drug-Target Binding Affinity for Drug Discovery and Development. - Zhijian Xu; Zhuo Yang; Yingtao Liu; Yunxiang Lu; Kaixian Chen; Weiliang Zhu (J. Chem. Inf. Model., 2014)

The Study and Improvement of Unidimensional Search about Nonlinear Optimization. - Yuhuan Cui; Jingguo Qu; Weiliang Zhu (J. Networks, 2014)

Algorithm and Its Implementation of Vehicle Safety Distance Control Based on the Numerical Simulation. - Jingguo Qu; Yuhuan Cui; Weiliang Zhu (J. Networks, 2014)

mD3DOCKxb: A Deep Parallel Optimized Software for Molecular Docking with Intel Xeon Phi Coprocessors. - Qian Cheng; Shaoliang Peng; Yutong Lu; Weiliang Zhu; Zhijian Xu; Xinben Zhang (CCGRID, 2015)

mAMBER: Accelerating Explicit Solvent Molecular Dynamic with Intel Xeon Phi Many-Integrated Core Coprocessors. - Xin Liu; Shaoliang Peng; Canqun Yang; Chengkun Wu; Haiqiang Wang; Qian Cheng; Weiliang Zhu; Jinan Wang (CCGRID, 2015)

A Method to Accelerate GROMACS in Offload Mode on Tianhe-2 Supercomputer. - Haiqiang Wang; Shaoliang Peng; Xiaoqian Zhu; Chengkun Wu; Xin Liu; Qian Chen; Weiliang Zhu; Jinan Wang; Huaiyu Yang (CCGRID, 2015)

mAMBER: A CPU/MIC collaborated parallel framework for AMBER on Tianhe-2 supercomputer. - Shaoliang Peng; Xiaoyu Zhang 008; Yutong Lu; Xiangke Liao; Kai Lu 001; Canqun Yang; Jie Liu 002; Weiliang Zhu; Dongqing Wei (BIBM, 2016)

mD3DOCKxb: An Ultra-Scalable CPU-MIC Coordinated Virtual Screening Framework. - Shaoliang Peng; Xiaoyu Zhang 008; Shunyun Yang; Wenhe Su; Zhiqiang Zhang; Dong Dong; Kai Lu 001; Yutong Lu; Xiangke Liao; Bertil Schmidt; Weiliang Zhu; Kuan-Ching Li (CCGrid, 2017)

The Underestimated Halogen Bonds Forming with Protein Side Chains in Drug Discovery and Design. - Qian Zhang 003; Zhijian Xu; Weiliang Zhu (J. Chem. Inf. Model., 2017)

Underestimated Halogen Bonds Forming with Protein Backbone in Protein Data Bank. - Qian Zhang 003; Zhijian Xu; Jiye Shi; Weiliang Zhu (J. Chem. Inf. Model., 2017)

Combined Virtual Screening and Substructure Search for Discovery of Novel FABP4 Inhibitors. - Haiyan Cai; Ting Wang; Zhuo Yang; Zhijian Xu; Guimin Wang; He-Yao Wang; Weiliang Zhu; Kaixian Chen (J. Chem. Inf. Model., 2017)

D3Pockets: A Method and Web Server for Systematic Analysis of Protein Pocket Dynamics. - Zhaoqiang Chen; Xinben Zhang; Cheng Peng; Jinan Wang; Zhijian Xu; Kaixian Chen; Jiye Shi; Weiliang Zhu (J. Chem. Inf. Model., 2019)

Underestimated Noncovalent Interactions in Protein Data Bank. - Zhijian Xu; Qian Zhang 003; Jiye Shi; Weiliang Zhu (J. Chem. Inf. Model., 2019)

Accurate prediction of relative binding affinities of a series of HIV-1 protease inhibitors using semi-empirical quantum mechanical charge. - Cheng Peng; Jinan Wang; Zhijian Xu; Tingting Cai; Weiliang Zhu (J. Comput. Chem., 2020)

Substitution Effect of the Trifluoromethyl Group on the Bioactivity in Medicinal Chemistry: Statistical Analysis and Energy Calculations. - Amina Abula; Zhijian Xu; Zhengdan Zhu; Cheng Peng; Zhaoqiang Chen; Weiliang Zhu; Haji Akber Aisa (J. Chem. Inf. Model., 2020)

Discovery of New and Potent InhA Inhibitors as Antituberculosis Agents: Structure-Based Virtual Screening Validated by Biological Assays and X-ray Crystallography. - Pharit Kamsri; Chayanin Hanwarinroj; Naruedon Phusi; Thimpika Pornprom; Kampanart Chayajarus; Auradee Punkvang; Nitima Suttipanta; Potjanee Srimanote; Khomson Suttisintong; Chomphunuch Songsiriritthigul; Patchreenart Saparpakorn; Supa Hannongbua; et al. (J. Chem. Inf. Model., 2020)

Interaction Nature and Computational Methods for Halogen Bonding: A Perspective. - Zhengdan Zhu; Zhijian Xu; Weiliang Zhu (J. Chem. Inf. Model., 2020)

High-Scalable Collaborated Parallel Framework for Large-Scale Molecular Dynamic Simulation on Tianhe-2 Supercomputer. - Shaoliang Peng; Xiaoyu Zhang 008; Wenhe Su; Dong Dong; Yutong Lu; Xiangke Liao; Kai Lu 001; Canqun Yang; Jie Liu 002; Weiliang Zhu; Dongqing Wei (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

Design of BRAVER - a bipedal robot actuated via proprioceptive electric motor. - Weiliang Zhu; Zhengguo Zhu; Xuewen Rong; Yibin Li 001; Guoteng Zhang (ROBIO, 2021)

Highly Dynamic Bipedal Locomotion via an Improved Virtual Model Algorithm. - Zhengguo Zhu; Weiliang Zhu; Zhongkai Sun; Yibin Li 001; Xuewen Rong; Guoteng Zhang (ROBIO, 2021)

Ligand-based approach for predicting drug targets and for virtual screening against COVID-19. - Yanqing Yang; Zhengdan Zhu; Xiaoyu Wang; Xinben Zhang; Kaijie Mu; Yulong Shi; Cheng Peng; Zhijian Xu; Weiliang Zhu (Briefings Bioinform., 2021)

D3DistalMutation: a Database to Explore the Effect of Distal Mutations on Enzyme Activity. - Xiaoyu Wang; Xinben Zhang; Cheng Peng; Yulong Shi; Huiyu Li; Zhijian Xu; Weiliang Zhu (J. Chem. Inf. Model., 2021)

Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. - Leyun Wu; Cheng Peng; Yanqing Yang; Yulong Shi; Liping Zhou; Zhijian Xu; Weiliang Zhu (Briefings Bioinform., 2022)

D3AI-CoV: a deep learning platform for predicting drug targets and for virtual screening against COVID-19. - Yanqing Yang; Deshan Zhou; Xinben Zhang; Yulong Shi; Jiaxin Han; Liping Zhou; Leyun Wu; Minfei Ma; Jintian Li; Shaoliang Peng; Zhijian Xu; Weiliang Zhu (Briefings Bioinform., 2022)

D3PM: a comprehensive database for protein motions ranging from residue to domain. - Cheng Peng; Xinben Zhang; Zhijian Xu; Zhaoqiang Chen; Yanqing Yang; Tingting Cai; Weiliang Zhu (BMC Bioinform., 2022)

D3AI-Spike: A deep learning platform for predicting binding affinity between SARS-CoV-2 spike receptor binding domain with multiple amino acid mutations and human angiotensin-converting enzyme 2. - Jiaxin Han; Tingting Liu; Xinben Zhang; Yanqing Yang; Yulong Shi; Jintian Li; Minfei Ma; Weiliang Zhu; Likun Gong; Zhijian Xu (Comput. Biol. Medicine, 2022)

Conserved protein targets for developing pan-coronavirus drugs based on sequence and 3D structure similarity analyses. - Minfei Ma; Yanqing Yang; Leyun Wu; Liping Zhou; Yulong Shi; Jiaxin Han; Zhijian Xu; Weiliang Zhu (Comput. Biol. Medicine, 2022)

Exploring the Binding Affinity and Mechanism between ACE2 and the Trimers of Delta and Omicron Spike Proteins by Molecular Dynamics Simulation and Bioassay. - Liping Zhou; Tingting Liu; Mengxia Mo; Yulong Shi; Leyun Wu; Yishui Li; Qiuping Qin; Weiliang Zhu; Chengkun Wu; Likun Gong; Zhijian Xu (J. Chem. Inf. Model., 2022)

Molecular dynamics study on the behavior and binding mechanism of target protein Transgelin-2 with its agonist TSG12 for anti-asthma drug discovery. - Leyun Wu; Guangpu Wang; Liping Zhou; Mengxia Mo; Yulong Shi; Bo Li; Leimiao Yin; Qiang Zhao; Yongqing Yang; Chengkun Wu; Zhijian Xu; Weiliang Zhu (Comput. Biol. Medicine, 2023)

D3CARP: a comprehensive platform with multiple-conformation based docking, ligand similarity search and deep learning approaches for target prediction and virtual screening. - Yulong Shi; Xinben Zhang; Yanqing Yang; Tingting Cai; Cheng Peng; Leyun Wu; Liping Zhou; Jiaxin Han; Minfei Ma; Weiliang Zhu; Zhijian Xu (Comput. Biol. Medicine, 2023)

Design and control of BRAVER: a bipedal robot actuated via proprioceptive electric motors. - Zhengguo Zhu; Weiliang Zhu; Guoteng Zhang; Teng Chen; Yibin Li 001; Xuewen Rong; Rui Song 002; Daoling Qin; Qiang Hua; Shugen Ma (Auton. Robots, 2023)

D3EGFR: a webserver for deep learning-guided drug sensitivity prediction and drug response information retrieval for EGFR mutation-driven lung cancer. - Yulong Shi; Chongwu Li; Xinben Zhang; Cheng Peng; Peng Sun; Qian Zhang; Leilei Wu; Ying Ding; Dong Xie; Zhijian Xu; Weiliang Zhu (Briefings Bioinform., 2024)

Unexpected effect of halogenation on the water solubility of small organic compounds. - Jianfang Zhang; Kinga Virág Gulyás; Jintian Li; Minfei Ma; Liping Zhou; Leyun Wu; Ruisheng Xiong; Mate Erdelyi; Weiliang Zhu; Zhijian Xu (Comput. Biol. Medicine, 2024)

D3Rings: A Fast and Accurate Method for Ring System Identification and Deep Generation of Drug-Like Cyclic Compounds. - Minfei Ma; Xinben Zhang; Liping Zhou; Zijian Han; Yulong Shi; Jintian Li; Leyun Wu; Zhijian Xu; Weiliang Zhu (J. Chem. Inf. Model., 2024)

A Heuristics-Based Reinforcement Learning Method to Control Bipedal Robots. - Daoling Qin; Guoteng Zhang; Zhengguo Zhu; Teng Chen; Weiliang Zhu; Xuewen Rong; Anhuan Xie; Yibin Li 001 (Int. J. Humanoid Robotics, 2024)