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2020 – today
- 2025
[j27]Yanlin Li, Wantong Jiao, Ruihan Liu, Xuejin Deng, Feng Zhu, Weiwei Xue:
Expanding the sequence spaces of synthetic binding protein using deep learning-based framework ProteinMPNN. Frontiers Comput. Sci. 19(5): 195903 (2025)- 2024
- [j26]Lingyan Zheng, Shuiyang Shi, Xiuna Sun, Mingkun Lu, Yang Liao, Sisi Zhu, Hongning Zhang
, Ziqi Pan, Pan Fang, Zhenyu Zeng, Honglin Li, Zhaorong Li, Weiwei Xue, Feng Zhu:
MoDAFold: a strategy for predicting the structure of missense mutant protein based on AlphaFold2 and molecular dynamics. Briefings Bioinform. 25(2) (2024) - [j25]Ding Luo, Zhuohao Tong, Lu Wen, Mingze Bai, Xiaojie Jin, Zerong Liu, Yinghong Li, Weiwei Xue:
DTNPD: A comprehensive database of drugs and targets for neurological and psychiatric disorders. Comput. Biol. Medicine 175: 108536 (2024) - [j24]Zhao Zhang, Fengcheng Li, Zixin Duan, Chaoqun Shi, Xiaona Wang, Feng Zhu, Weiwei Xue:
OPTICS: An interactive online platform for photosensory and bio-functional proteins in optogenetic systems. Comput. Biol. Medicine 178: 108687 (2024) - [j23]Xiaojie Jin, Min Zhang, Beibei Fu, Mi Li, Jingyi Yang, Zhiming Zhang, Chenghao Li, Huijuan Zhang, Haibo Wu, Weiwei Xue, Yongqi Liu:
Structure-Based Discovery of the SARS-CoV-2 Main Protease Noncovalent Inhibitors from Traditional Chinese Medicine. J. Chem. Inf. Model. 64(4): 1319-1330 (2024) - [j22]Gao Tu, Tingting Fu, Guoxun Zheng, Binbin Xu, Rongpei Gou, Ding Luo, Panpan Wang, Weiwei Xue:
Computational Chemistry in Structure-Based Solute Carrier Transporter Drug Design: Recent Advances and Future Perspectives. J. Chem. Inf. Model. 64(5): 1433-1455 (2024) - [j21]Rongpei Gou, Jingyi Yang, Menghan Guo, Yingjun Chen, Weiwei Xue:
CNSMolGen: A Bidirectional Recurrent Neural Network-Based Generative Model for De Novo Central Nervous System Drug Design. J. Chem. Inf. Model. 64(10): 4059-4070 (2024) - [j20]Jingyi Yang, Beibei Fu, Rongpei Gou, Xiaoyuan Lin, Haibo Wu, Weiwei Xue:
Molecular Mechanism-Driven Discovery of Novel Small Molecule Inhibitors against Drug-Resistant SARS-CoV-2 Mpro Variants. J. Chem. Inf. Model. 64(20): 7998-8009 (2024) - 2023
- [j19]Qingqing Du, Gao Tu, Yan Qian, Jingyi Yang, Xiaojun Yao, Weiwei Xue:
Unbiased molecular dynamics simulation of a first-in-class small molecule inhibitor binds to oncostatin M. Comput. Biol. Medicine 155: 106709 (2023) - [j18]Arzu Mijit, Xiaona Wang, Yanlin Li, Hangwei Xu, Yingjun Chen, Weiwei Xue:
Mapping synthetic binding proteins epitopes on diverse protein targets by protein structure prediction and protein-protein docking. Comput. Biol. Medicine 163: 107183 (2023) - [j17]Shengzhe Deng, Haiwei Zhang, Rongpei Gou, Ding Luo, Zerong Liu, Feng Zhu, Weiwei Xue:
Structure-Based Discovery of a Novel Allosteric Inhibitor against Human Dopamine Transporter. J. Chem. Inf. Model. 63(14): 4458-4467 (2023) - 2022
- [j16]Xiangben Hu, Zhichen Hu, Jielin Jiang, Weiwei Xue, Xiumian Hu, Xiaolong Xu:
Character embedding-based Bi-LSTM for Zircon similarity calculation with clustering. Earth Sci. Informatics 15(3): 1417-1425 (2022) - [j15]Xiaona Wang, Fengcheng Li, Wenqi Qiu, Binbin Xu, Yanlin Li, Xichen Lian, Hongyan Yu, Zhao Zhang, Jianxin Wang, Zhaorong Li, Weiwei Xue, Feng Zhu:
SYNBIP: synthetic binding proteins for research, diagnosis and therapy. Nucleic Acids Res. 50(D1): 560-570 (2022) - 2021
- [j14]Jingyi Yang, Xiaoyuan Lin, Na Xing, Zhao Zhang, Haiwei Zhang, Haibo Wu, Weiwei Xue:
Structure-Based Discovery of Novel Nonpeptide Inhibitors Targeting SARS-CoV-2 Mpro. J. Chem. Inf. Model. 61(8): 3917-3926 (2021) - [j13]Jing Tang, Xianglu Wu, Minjie Mou, Chuan Wang, Lidan Wang, Fengcheng Li, Maiyuan Guo, Jiayi Yin, Wenqin Xie, Xiaona Wang, Yingxiong Wang, Yubin Ding, Weiwei Xue, Feng Zhu:
GIMICA: host genetic and immune factors shaping human microbiota. Nucleic Acids Res. 49(Database-Issue): D715-D722 (2021) - 2020
- [j12]Jing Tang, Jianbo Fu, Yunxia Wang, Bo Li, Yinghong Li, Qingxia Yang, Xuejiao Cui, Jiajun Hong, Xiaofeng Li, Yuzong Chen, Weiwei Xue, Feng Zhu:
ANPELA: analysis and performance assessment of the label-free quantification workflow for metaproteomic studies. Briefings Bioinform. 21(2): 621-636 (2020) - [j11]Ying Hong Li, Xiao Xu Li, Jiajun Hong, Yunxia Wang, Jianbo Fu, Hong Yang, Chun Yan Yu, Feng Cheng Li, Jie Hu, Weiwei Xue, Yu Yang Jiang, Yuzong Chen, Feng Zhu:
Clinical trials, progression-speed differentiating features and swiftness rule of the innovative targets of first-in-class drugs. Briefings Bioinform. 21(2): 649-662 (2020) - [j10]Zhijie Han, Weiwei Xue, Lin Tao, Yan Lou, Yunqing Qiu, Feng Zhu:
Genome-wide identification and analysis of the eQTL lncRNAs in multiple sclerosis based on RNA-seq data. Briefings Bioinform. 21(3): 1023-1037 (2020) - [j9]Qingxia Yang, Bo Li, Jing Tang, Xuejiao Cui, Yunxia Wang, Xiaofeng Li, Jie Hu, Yuzong Chen, Weiwei Xue, Yan Lou, Yunqing Qiu, Feng Zhu:
Consistent gene signature of schizophrenia identified by a novel feature selection strategy from comprehensive sets of transcriptomic data. Briefings Bioinform. 21(3): 1058-1068 (2020) - [j8]Jing Tang, Yunxia Wang, Jianbo Fu, Ying Zhou, Yongchao Luo, Ying Zhang, Bo Li, Qingxia Yang, Weiwei Xue, Yan Lou, Yunqing Qiu, Feng Zhu:
A critical assessment of the feature selection methods used for biomarker discovery in current metaproteomics studies. Briefings Bioinform. 21(4): 1378-1390 (2020) - [j7]Jiajun Hong, Yongchao Luo, Yang Zhang, Junbiao Ying, Weiwei Xue, Tian Xie, Lin Tao, Feng Zhu:
Protein functional annotation of simultaneously improved stability, accuracy and false discovery rate achieved by a sequence-based deep learning. Briefings Bioinform. 21(4): 1437-1447 (2020) - [j6]Jiajun Hong, Yongchao Luo, Minjie Mou, Jianbo Fu, Yang Zhang, Weiwei Xue, Tian Xie, Lin Tao, Yan Lou, Feng Zhu:
Convolutional neural network-based annotation of bacterial type IV secretion system effectors with enhanced accuracy and reduced false discovery. Briefings Bioinform. 21(5): 1825-1836 (2020) - [j5]Qingxia Yang, Jiajun Hong, Yi Li, Weiwei Xue, Song Li, Hui Yang, Feng Zhu:
A novel bioinformatics approach to identify the consistently well-performing normalization strategy for current metabolomic studies. Briefings Bioinform. 21(6): 2142-2152 (2020)
2010 – 2019
- 2017
- [j4]Bo Li, Jing Tang, Qingxia Yang, Shuang Li, Xuejiao Cui, Yinghong Li, Yuzong Chen, Weiwei Xue, Xiaofeng Li, Feng Zhu:
NOREVA: normalization and evaluation of MS-based metabolomics data. Nucleic Acids Res. 45(Webserver-Issue): W162-W170 (2017) - 2014
- [j3]Weiwei Xue, Yihe Ban, Huanxiang Liu, Xiaojun Yao:
Computational Study on the Drug Resistance Mechanism against HCV NS3/4A Protease Inhibitors Vaniprevir and MK-5172 by the Combination Use of Molecular Dynamics Simulation, Residue Interaction Network, and Substrate Envelope Analysis. J. Chem. Inf. Model. 54(2): 621-633 (2014) - 2013
- [j2]Weiwei Xue, Xiaojie Jin, Lulu Ning, Meixia Wang, Huanxiang Liu, Xiaojun Yao:
Exploring the Molecular Mechanism of Cross-Resistance to HIV-1 Integrase Strand Transfer Inhibitors by Molecular Dynamics Simulation and Residue Interaction Network Analysis. J. Chem. Inf. Model. 53(1): 210-222 (2013) - 2012
- [j1]Weiwei Xue, Huanxiang Liu, Xiaojun Yao:
Molecular mechanism of HIV-1 integrase-vDNA interactions and strand transfer inhibitor action: A molecular modeling perspective. J. Comput. Chem. 33(5): 527-536 (2012)
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