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Weiliang Zhu
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2020 – today
- 2024
- [j44]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) - [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)
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