Molecular mechanism of HIV-1 integrase-vDNA interactions and strand transfer inhibitor action: A molecular modeling perspective. - Weiwei Xue; Huanxiang Liu; Xiaojun Yao (J. Comput. Chem., 2012)

Exploring the Molecular Mechanism of Cross-Resistance to HIV-1 Integrase Strand Transfer Inhibitors by Molecular Dynamics Simulation and Residue Interaction Network Analysis. - Weiwei Xue; Xiaojie Jin; Lulu Ning; Meixia Wang; Huanxiang Liu; Xiaojun Yao (J. Chem. Inf. Model., 2013)

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. - Weiwei Xue; Yihe Ban; Huanxiang Liu; Xiaojun Yao (J. Chem. Inf. Model., 2014)

NOREVA: normalization and evaluation of MS-based metabolomics data. - Bo Li 093; Jing Tang; Qingxia Yang; Shuang Li; Xuejiao Cui; Yinghong Li 002; Yuzong Chen 002; Weiwei Xue; Xiaofeng Li; Feng Zhu 004 (Nucleic Acids Res., 2017)

Genome-wide identification and analysis of the eQTL lncRNAs in multiple sclerosis based on RNA-seq data. - Zhijie Han 002; Weiwei Xue; Lin Tao; Yan Lou; Yunqing Qiu; Feng Zhu 004 (Briefings Bioinform., 2020)

Convolutional neural network-based annotation of bacterial type IV secretion system effectors with enhanced accuracy and reduced false discovery. - Jiajun Hong; Yongchao Luo; Minjie Mou; Jianbo Fu; Yang Zhang 125; Weiwei Xue; Tian Xie; Lin Tao; Yan Lou; Feng Zhu 004 (Briefings Bioinform., 2020)

Protein functional annotation of simultaneously improved stability, accuracy and false discovery rate achieved by a sequence-based deep learning. - Jiajun Hong; Yongchao Luo; Yang Zhang 125; Junbiao Ying; Weiwei Xue; Tian Xie; Lin Tao; Feng Zhu 004 (Briefings Bioinform., 2020)

Clinical trials, progression-speed differentiating features and swiftness rule of the innovative targets of first-in-class drugs. - Ying Hong Li 002; Xiao Xu Li; Jiajun Hong; Yunxia Wang; Jianbo Fu; Hong Yang; Chun Yan Yu; Feng Cheng Li; Jie Hu 020; Weiwei Xue; Yu Yang Jiang; Yuzong Chen 002; et al. (Briefings Bioinform., 2020)

ANPELA: analysis and performance assessment of the label-free quantification workflow for metaproteomic studies. - Jing Tang; Jianbo Fu; Yunxia Wang; Bo Li 093; Yinghong Li 002; Qingxia Yang; Xuejiao Cui; Jiajun Hong; Xiaofeng Li; Yuzong Chen 002; Weiwei Xue; Feng Zhu 004 (Briefings Bioinform., 2020)

A critical assessment of the feature selection methods used for biomarker discovery in current metaproteomics studies. - Jing Tang; Yunxia Wang; Jianbo Fu; Ying Zhou; Yongchao Luo; Ying Zhang 061; Bo Li 093; Qingxia Yang; Weiwei Xue; Yan Lou; Yunqing Qiu; Feng Zhu 004 (Briefings Bioinform., 2020)

A novel bioinformatics approach to identify the consistently well-performing normalization strategy for current metabolomic studies. - Qingxia Yang; Jiajun Hong; Yi Li; Weiwei Xue; Song Li; Hui Yang; Feng Zhu 004 (Briefings Bioinform., 2020)

Consistent gene signature of schizophrenia identified by a novel feature selection strategy from comprehensive sets of transcriptomic data. - Qingxia Yang; Bo Li 093; Jing Tang; Xuejiao Cui; Yunxia Wang; Xiaofeng Li; Jie Hu 020; Yuzong Chen 002; Weiwei Xue; Yan Lou; Yunqing Qiu; Feng Zhu 004 (Briefings Bioinform., 2020)

Structure-Based Discovery of Novel Nonpeptide Inhibitors Targeting SARS-CoV-2 Mpro. - Jingyi Yang; Xiaoyuan Lin; Na Xing; Zhao Zhang; Haiwei Zhang; Haibo Wu 005; Weiwei Xue (J. Chem. Inf. Model., 2021)

GIMICA: host genetic and immune factors shaping human microbiota. - Jing Tang; Xianglu Wu; Minjie Mou; Chuan Wang; Lidan Wang; Fengcheng Li; Maiyuan Guo; Jiayi Yin; Wenqin Xie; Xiaona Wang; Yingxiong Wang; Yubin Ding; et al. (Nucleic Acids Res., 2021)

Character embedding-based Bi-LSTM for Zircon similarity calculation with clustering. - Xiangben Hu; Zhichen Hu; Jielin Jiang; Weiwei Xue; Xiumian Hu; Xiaolong Xu 001 (Earth Sci. Informatics, 2022)

SYNBIP: synthetic binding proteins for research, diagnosis and therapy. - Xiaona Wang; Fengcheng Li; Wenqi Qiu 003; Binbin Xu; Yanlin Li; Xichen Lian; Hongyan Yu; Zhao Zhang; Jianxin Wang 001; Zhaorong Li; Weiwei Xue; Feng Zhu 004 (Nucleic Acids Res., 2022)

Unbiased molecular dynamics simulation of a first-in-class small molecule inhibitor binds to oncostatin M. - Qingqing Du; Gao Tu; Yan Qian; Jingyi Yang; Xiaojun Yao; Weiwei Xue (Comput. Biol. Medicine, 2023)

Structure-Based Discovery of a Novel Allosteric Inhibitor against Human Dopamine Transporter. - Shengzhe Deng; Haiwei Zhang; Rongpei Gou; Ding Luo; Zerong Liu; Feng Zhu 004; Weiwei Xue (J. Chem. Inf. Model., 2023)

Mapping synthetic binding proteins epitopes on diverse protein targets by protein structure prediction and protein-protein docking. - Arzu Mijit; Xiaona Wang; Yanlin Li; Hangwei Xu; Yingjun Chen; Weiwei Xue (Comput. Biol. Medicine, 2023)

DTNPD: A comprehensive database of drugs and targets for neurological and psychiatric disorders. - Ding Luo; Zhuohao Tong; Lu Wen; Mingze Bai; Xiaojie Jin; Zerong Liu; Yinghong Li 002; Weiwei Xue (Comput. Biol. Medicine, 2024)

OPTICS: An interactive online platform for photosensory and bio-functional proteins in optogenetic systems. - Zhao Zhang; Fengcheng Li; Zixin Duan; Chaoqun Shi; Xiaona Wang; Feng Zhu 004; Weiwei Xue (Comput. Biol. Medicine, 2024)

CNSMolGen: A Bidirectional Recurrent Neural Network-Based Generative Model for De Novo Central Nervous System Drug Design. - Rongpei Gou; Jingyi Yang; Menghan Guo; Yingjun Chen; Weiwei Xue (J. Chem. Inf. Model., 2024)

Molecular Mechanism-Driven Discovery of Novel Small Molecule Inhibitors against Drug-Resistant SARS-CoV-2 Mpro Variants. - Jingyi Yang; Beibei Fu; Rongpei Gou; Xiaoyuan Lin; Haibo Wu 005; Weiwei Xue (J. Chem. Inf. Model., 2024)

MoDAFold: a strategy for predicting the structure of missense mutant protein based on AlphaFold2 and molecular dynamics. - Lingyan Zheng; Shuiyang Shi; Xiuna Sun; Mingkun Lu; Yang Liao; Sisi Zhu; Hongning Zhang; Ziqi Pan; Pan Fang; Zhenyu Zeng; Honglin Li 003; Zhaorong Li; et al. (Briefings Bioinform., 2024)

Structure-Based Discovery of the SARS-CoV-2 Main Protease Noncovalent Inhibitors from Traditional Chinese Medicine. - Xiaojie Jin; Min Zhang; Beibei Fu; Mi Li; Jingyi Yang; Zhiming Zhang; Chenghao Li; Huijuan Zhang; Haibo Wu 005; Weiwei Xue; Yongqi Liu (J. Chem. Inf. Model., 2024)

Computational Chemistry in Structure-Based Solute Carrier Transporter Drug Design: Recent Advances and Future Perspectives. - Gao Tu; Tingting Fu; Guoxun Zheng; Binbin Xu; Rongpei Gou; Ding Luo; Panpan Wang; Weiwei Xue (J. Chem. Inf. Model., 2024)

Expanding the sequence spaces of synthetic binding protein using deep learning-based framework ProteinMPNN. - Yanlin Li; Wantong Jiao; Ruihan Liu; Xuejin Deng; Feng Zhu 004; Weiwei Xue (Frontiers Comput. Sci., 2025)

ConoDL: a deep learning framework for rapid generation and prediction of conotoxins. - Menghan Guo; Zengpeng Li; Xuejin Deng; Ding Luo; Jingyi Yang; Yingjun Chen; Weiwei Xue (J. Comput. Aided Mol. Des., 2025)