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2020 – today
- 2024
[j45]Jianfang Zhang, Kinga Virág Gulyás, Jintian Li, Minfei Ma, Liping Zhou, Leyun Wu, Ruisheng Xiong, Mate Erdelyi, Weiliang Zhu, Zhijian Xu
:
Unexpected effect of halogenation on the water solubility of small organic compounds. Comput. Biol. Medicine 172: 108209 (2024)- [j44]Daoling Qin, Guoteng Zhang, Zhengguo Zhu, Teng Chen, Weiliang Zhu, Xuewen Rong, Anhuan Xie, Yibin Li:
A Heuristics-Based Reinforcement Learning Method to Control Bipedal Robots. Int. J. Humanoid Robotics 21(3): 2350013:1-2350013:22 (2024) - [j43]Minfei Ma, Xinben Zhang, Liping Zhou, Zijian Han, Yulong Shi, Jintian Li, Leyun Wu, Zhijian Xu, Weiliang Zhu:
D3Rings: A Fast and Accurate Method for Ring System Identification and Deep Generation of Drug-Like Cyclic Compounds. J. Chem. Inf. Model. 64(3): 724-736 (2024) - 2023
- [j42]Zhengguo Zhu, Weiliang Zhu, Guoteng Zhang, Teng Chen, Yibin Li, Xuewen Rong, Rui Song, Daoling Qin, Qiang Hua, Shugen Ma:
Design and control of BRAVER: a bipedal robot actuated via proprioceptive electric motors. Auton. Robots 47(8): 1229-1243 (2023) - [j41]Leyun Wu, Guangpu Wang, Liping Zhou, Mengxia Mo, Yulong Shi, Bo Li, Leimiao Yin, Qiang Zhao, Yongqing Yang, Chengkun Wu, Zhijian Xu, Weiliang Zhu:
Molecular dynamics study on the behavior and binding mechanism of target protein Transgelin-2 with its agonist TSG12 for anti-asthma drug discovery. Comput. Biol. Medicine 153: 106515 (2023) - [j40]Yulong Shi, Xinben Zhang, Yanqing Yang, Tingting Cai, Cheng Peng, Leyun Wu, Liping Zhou, Jiaxin Han, Minfei Ma, Weiliang Zhu, Zhijian Xu:
D3CARP: a comprehensive platform with multiple-conformation based docking, ligand similarity search and deep learning approaches for target prediction and virtual screening. Comput. Biol. Medicine 164: 107283 (2023) - 2022
- [j39]Leyun Wu, Cheng Peng, Yanqing Yang, Yulong Shi, Liping Zhou, Zhijian Xu, Weiliang Zhu:
Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. Briefings Bioinform. 23(1) (2022) - [j38]Yanqing Yang, Deshan Zhou, Xinben Zhang, Yulong Shi, Jiaxin Han, Liping Zhou, Leyun Wu, Minfei Ma, Jintian Li, Shaoliang Peng, Zhijian Xu, Weiliang Zhu:
D3AI-CoV: a deep learning platform for predicting drug targets and for virtual screening against COVID-19. Briefings Bioinform. 23(3) (2022) - [j37]Cheng Peng, Xinben Zhang, Zhijian Xu, Zhaoqiang Chen, Yanqing Yang, Tingting Cai, Weiliang Zhu:
D3PM: a comprehensive database for protein motions ranging from residue to domain. BMC Bioinform. 23(1): 70 (2022) - [j36]Minfei Ma, Yanqing Yang, Leyun Wu, Liping Zhou, Yulong Shi, Jiaxin Han, Zhijian Xu, Weiliang Zhu:
Conserved protein targets for developing pan-coronavirus drugs based on sequence and 3D structure similarity analyses. Comput. Biol. Medicine 145: 105455 (2022) - [j35]Jiaxin Han, Tingting Liu, Xinben Zhang, Yanqing Yang, Yulong Shi, Jintian Li, Minfei Ma, Weiliang Zhu, Likun Gong, Zhijian Xu:
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. Comput. Biol. Medicine 151(Part): 106212 (2022) - [j34]Liping Zhou, Tingting Liu, Mengxia Mo, Yulong Shi, Leyun Wu, Yishui Li, Qiuping Qin, Weiliang Zhu, Chengkun Wu, Likun Gong, Zhijian Xu:
Exploring the Binding Affinity and Mechanism between ACE2 and the Trimers of Delta and Omicron Spike Proteins by Molecular Dynamics Simulation and Bioassay. J. Chem. Inf. Model. 62(18): 4512-4522 (2022) - 2021
- [j33]Yanqing Yang, Zhengdan Zhu, Xiaoyu Wang, Xinben Zhang, Kaijie Mu, Yulong Shi, Cheng Peng, Zhijian Xu, Weiliang Zhu:
Ligand-based approach for predicting drug targets and for virtual screening against COVID-19. Briefings Bioinform. 22(2): 1053-1064 (2021) - [j32]Xiaoyu Wang, Xinben Zhang, Cheng Peng, Yulong Shi, Huiyu Li, Zhijian Xu, Weiliang Zhu:
D3DistalMutation: a Database to Explore the Effect of Distal Mutations on Enzyme Activity. J. Chem. Inf. Model. 61(5): 2499-2508 (2021) - [c7]Zhengguo Zhu, Weiliang Zhu, Zhongkai Sun, Yibin Li, Xuewen Rong, Guoteng Zhang:
Highly Dynamic Bipedal Locomotion via an Improved Virtual Model Algorithm. ROBIO 2021: 1010-1015 - [c6]Weiliang Zhu, Zhengguo Zhu, Xuewen Rong, Yibin Li, Guoteng Zhang:
Design of BRAVER - a bipedal robot actuated via proprioceptive electric motor. ROBIO 2021: 1046-1051 - 2020
- [j31]Cheng Peng, Jinan Wang, Zhijian Xu, Tingting Cai, Weiliang Zhu:
Accurate prediction of relative binding affinities of a series of HIV-1 protease inhibitors using semi-empirical quantum mechanical charge. J. Comput. Chem. 41(19): 1773-1780 (2020) - [j30]Pharit Kamsri, Chayanin Hanwarinroj, Naruedon Phusi, Thimpika Pornprom, Kampanart Chayajarus, Auradee Punkvang, Nitima Suttipanta, Potjanee Srimanote, Khomson Suttisintong, Chomphunuch Songsiriritthigul, Patchreenart Saparpakorn, Supa Hannongbua, Siriluk Rattanabunyong, Supaporn Seetaha, Kiattawee Choowongkomon, Sanya Sureram, Prasat Kittakoop, Poonpilas Hongmanee, Pitak Santanirand, Zhaoqiang Chen, Weiliang Zhu, Rosemary A. Blood, Yuiko Takebayashi, Philip Hinchliffe, Adrian J. Mulholland, James Spencer, Pornpan Pungpo:
Discovery of New and Potent InhA Inhibitors as Antituberculosis Agents: Structure-Based Virtual Screening Validated by Biological Assays and X-ray Crystallography. J. Chem. Inf. Model. 60(1): 226-234 (2020) - [j29]Zhengdan Zhu, Zhijian Xu, Weiliang Zhu:
Interaction Nature and Computational Methods for Halogen Bonding: A Perspective. J. Chem. Inf. Model. 60(6): 2683-2696 (2020) - [j28]Amina Abula, Zhijian Xu, Zhengdan Zhu, Cheng Peng, Zhaoqiang Chen, Weiliang Zhu, Haji Akber Aisa:
Substitution Effect of the Trifluoromethyl Group on the Bioactivity in Medicinal Chemistry: Statistical Analysis and Energy Calculations. J. Chem. Inf. Model. 60(12): 6242-6250 (2020) - [j27]Shaoliang Peng, Xiaoyu Zhang, Wenhe Su, Dong Dong, Yutong Lu, Xiangke Liao, Kai Lu, Canqun Yang, Jie Liu, Weiliang Zhu, Dongqing Wei:
High-Scalable Collaborated Parallel Framework for Large-Scale Molecular Dynamic Simulation on Tianhe-2 Supercomputer. IEEE ACM Trans. Comput. Biol. Bioinform. 17(3): 804-816 (2020)
2010 – 2019
- 2019
- [j26]Zhaoqiang Chen, Xinben Zhang, Cheng Peng, Jinan Wang, Zhijian Xu, Kaixian Chen, Jiye Shi, Weiliang Zhu:
D3Pockets: A Method and Web Server for Systematic Analysis of Protein Pocket Dynamics. J. Chem. Inf. Model. 59(8): 3353-3358 (2019) - [j25]Zhijian Xu, Qian Zhang, Jiye Shi, Weiliang Zhu:
Underestimated Noncovalent Interactions in Protein Data Bank. J. Chem. Inf. Model. 59(8): 3389-3399 (2019) - 2017
- [j24]Qian Zhang, Zhijian Xu, Weiliang Zhu:
The Underestimated Halogen Bonds Forming with Protein Side Chains in Drug Discovery and Design. J. Chem. Inf. Model. 57(1): 22-26 (2017) - [j23]Qian Zhang, Zhijian Xu, Jiye Shi, Weiliang Zhu:
Underestimated Halogen Bonds Forming with Protein Backbone in Protein Data Bank. J. Chem. Inf. Model. 57(7): 1529-1534 (2017) - [j22]Haiyan Cai, Ting Wang, Zhuo Yang, Zhijian Xu, Guimin Wang, He-Yao Wang, Weiliang Zhu, Kaixian Chen:
Combined Virtual Screening and Substructure Search for Discovery of Novel FABP4 Inhibitors. J. Chem. Inf. Model. 57(9): 2329-2335 (2017) - [c5]Shaoliang Peng, Xiaoyu Zhang, Shunyun Yang, Wenhe Su, Zhiqiang Zhang, Dong Dong, Kai Lu, Yutong Lu, Xiangke Liao, Bertil Schmidt, Weiliang Zhu, Kuan-Ching Li:
mD3DOCKxb: An Ultra-Scalable CPU-MIC Coordinated Virtual Screening Framework. CCGrid 2017: 671-676 - 2016
- [c4]Shaoliang Peng, Xiaoyu Zhang, Yutong Lu, Xiangke Liao, Kai Lu, Canqun Yang, Jie Liu, Weiliang Zhu, Dongqing Wei:
mAMBER: A CPU/MIC collaborated parallel framework for AMBER on Tianhe-2 supercomputer. BIBM 2016: 651-657 - 2015
- [c3]Qian Cheng, Shaoliang Peng, Yutong Lu, Weiliang Zhu, Zhijian Xu, Xinben Zhang:
mD3DOCKxb: A Deep Parallel Optimized Software for Molecular Docking with Intel Xeon Phi Coprocessors. CCGRID 2015: 725-728 - [c2]Xin Liu, Shaoliang Peng, Canqun Yang, Chengkun Wu, Haiqiang Wang, Qian Cheng, Weiliang Zhu, Jinan Wang:
mAMBER: Accelerating Explicit Solvent Molecular Dynamic with Intel Xeon Phi Many-Integrated Core Coprocessors. CCGRID 2015: 729-732 - [c1]Haiqiang Wang, Shaoliang Peng, Xiaoqian Zhu, Chengkun Wu, Xin Liu, Qian Chen, Weiliang Zhu, Jinan Wang, Huaiyu Yang:
A Method to Accelerate GROMACS in Offload Mode on Tianhe-2 Supercomputer. CCGRID 2015: 781-784 - 2014
- [j21]Jianlong Peng, Jing Lu, Qiancheng Shen, Mingyue Zheng, Xiaomin Luo, Weiliang Zhu, Hualiang Jiang, Kaixian Chen:
In silico site of metabolism prediction for human UGT-catalyzed reactions. Bioinform. 30(3): 398-405 (2014) - [j20]Jing Lu, Jianlong Peng, Jinan Wang, Qiancheng Shen, Yi Bi, Likun Gong, Mingyue Zheng, Xiaomin Luo, Weiliang Zhu, Hualiang Jiang, Kaixian Chen:
Estimation of acute oral toxicity in rat using local lazy learning. J. Cheminformatics 6(1): 26 (2014) - [j19]Zhijian Xu, Zhuo Yang, Yingtao Liu, Yunxiang Lu, Kaixian Chen, Weiliang Zhu:
Halogen Bond: Its Role beyond Drug-Target Binding Affinity for Drug Discovery and Development. J. Chem. Inf. Model. 54(1): 69-78 (2014) - [j18]Jingguo Qu, Yuhuan Cui, Weiliang Zhu:
Algorithm and Its Implementation of Vehicle Safety Distance Control Based on the Numerical Simulation. J. Networks 9(12): 3486-3493 (2014) - [j17]Yuhuan Cui, Jingguo Qu, Weiliang Zhu:
The Study and Improvement of Unidimensional Search about Nonlinear Optimization. J. Networks 9(12): 3494-3501 (2014) - 2013
- [j16]Jianzhong Chen, Jinan Wang, Weiliang Zhu, Guohui Li:
A computational analysis of binding modes and conformation changes of MDM2 induced by p53 and inhibitor bindings. J. Comput. Aided Mol. Des. 27(11): 965-974 (2013) - [j15]Di Wang, Xuelian Zhu, Changjun Cui, Mei Dong, Hualiang Jiang, Zhengming Li, Zhen Liu, Weiliang Zhu, Jianguo Wang:
Discovery of Novel Acetohydroxyacid Synthase Inhibitors as Active Agents against Mycobacterium tuberculosis by Virtual Screening and Bioassay. J. Chem. Inf. Model. 53(2): 343-353 (2013) - 2012
- [j14]Yong Wang, Jing Lu, Fei Wang, Qiancheng Shen, Mingyue Zheng, Xiaomin Luo, Weiliang Zhu, Hualiang Jiang, Kaixian Chen:
Estimation of Carcinogenicity Using Molecular Fragments Tree. J. Chem. Inf. Model. 52(8): 1994-2003 (2012) - 2011
- [j13]Qiancheng Shen, Bing Xiong, Mingyue Zheng, Xiaomin Luo, Cheng Luo, Xian Liu, Yun Du, Jing Li, Weiliang Zhu, Jingkang Shen, Hualiang Jiang:
Knowledge-Based Scoring Functions in Drug Design: 2. Can the Knowledge Base Be Enriched? J. Chem. Inf. Model. 51(2): 386-397 (2011) - [j12]Fei Wang, DongXiang Liu, Heyao Wang, Cheng Luo, Mingyue Zheng, Hong Liu, Weiliang Zhu, Xiaomin Luo, Jian Zhang, Hualiang Jiang:
Computational Screening for Active Compounds Targeting Protein Sequences: Methodology and Experimental Validation. J. Chem. Inf. Model. 51(11): 2821-2828 (2011) - [j11]Mingyue Zheng, Bing Xiong, Cheng Luo, Shanshan Li, Xian Liu, Qiancheng Shen, Jing Li, Weiliang Zhu, Xiaomin Luo, Hualiang Jiang:
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. 51(11): 2994-3004 (2011) - 2010
- [j10]Zhi Chen, Guanghui Tian, Zhen Wang, Hualiang Jiang, Jingshan Shen, Weiliang Zhu:
Multiple Pharmacophore Models Combined with Molecular Docking: A Reliable Way for Efficiently Identifying Novel PDE4 Inhibitors with High Structural Diversity. J. Chem. Inf. Model. 50(4): 615-625 (2010)
2000 – 2009
- 2009
- [j9]Mingyue Zheng, Xiaomin Luo, Qiancheng Shen, Yong Wang, Yun Du, Weiliang Zhu, Hualiang Jiang:
Site of metabolism prediction for six biotransformations mediated by cytochromes P450. Bioinform. 25(10): 1251-1258 (2009) - 2008
- [j8]Zhenting Gao, Honglin Li, Hailei Zhang, Xiaofeng Liu, Ling Kang, Xiaomin Luo, Weiliang Zhu, Kaixian Chen, Xicheng Wang, Hualiang Jiang:
PDTD: a web-accessible protein database for drug target identification. BMC Bioinform. 9 (2008) - [j7]Xiaoyu Zhao, Xiaofeng Liu, Yuanyuan Wang, Zhi Chen, Ling Kang, Hailei Zhang, Xiaomin Luo, Weiliang Zhu, Kaixian Chen, Honglin Li, Xicheng Wang, Hualiang Jiang:
An Improved PMF Scoring Function for Universally Predicting the Interactions of a Ligand with Protein, DNA, and RNA. J. Chem. Inf. Model. 48(7): 1438-1447 (2008) - 2007
- [j6]Zhili Zuo, Chen Gang, Hanjun Zou, Puah Chum Mok, Weiliang Zhu, Kaixian Chen, Hualiang Jiang:
Why does beta-secretase zymogen possess catalytic activity? Molecular modeling and molecular dynamics simulation studies. Comput. Biol. Chem. 31(3): 186-195 (2007) - 2006
- [j5]Mingyue Zheng, Zhiguo Liu, Chunxia Xue, Weiliang Zhu, Kaixian Chen, Xiaomin Luo, Hualiang Jiang:
Mutagenic probability estimation of chemical compounds by a novel molecular electrophilicity vector and support vector machine. Bioinform. 22(17): 2099-2106 (2006) - [j4]Zhenshan Zhang, Mingyue Zheng, Li Du, Jianhua Shen, Xiaomin Luo, Weiliang Zhu, Hualiang Jiang:
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. 20(5): 281-293 (2006) - [j3]Mingyue Zheng, Kunqian Yu, Hong Liu, Xiaomin Luo, Kaixian Chen, Weiliang Zhu, Hualiang Jiang:
QSAR analyses on avian influenza virus neuraminidase inhibitors using CoMFA, CoMSIA, and HQSAR. J. Comput. Aided Mol. Des. 20(9): 549-566 (2006) - [j2]Honglin Li, Zhenting Gao, Ling Kang, Hailei Zhang, Kun Yang, Kunqian Yu, Xiaomin Luo, Weiliang Zhu, Kaixian Chen, Jianhua Shen, Xicheng Wang, Hualiang Jiang:
TarFisDock: a web server for identifying drug targets with docking approach. Nucleic Acids Res. 34(Web-Server-Issue): 219-224 (2006) - 2005
- [j1]Suxin Zheng, Xiaomin Luo, Gang Chen, Weiliang Zhu, Jianhua Shen, Kaixian Chen, Hualiang Jiang:
A New Rapid and Effective Chemistry Space Filter in Recognizing a Druglike Database. J. Chem. Inf. Model. 45(4): 856-862 (2005)
Coauthor Index
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