XZ
Xujun Zhang
Drug DiscoveryProteinsq-bio.BMmachine learningMachine LearningNeural Networks, Computerdeep learningvirtual screeningVirtual screeningcs.LG
On Valency
published · living versionsW_pt4vphpn·v1 · currentpublished
W_5dheks5m·v1published
Preprints & journals
75 papers in the corpus · 2014–2026Facilitating structure-based drug discovery with an artificial intelligence-driven virtual screening platform.42342989 · Gu, Shukai, Zhang, Xujun, Xiao, Mengwu et al.2026 · 1 citationNature protocols. 2026
Computational and AI-Driven Ecosystem for Structure-Based Covalent Drug Discovery.41758998 · Li, Shi, Du, Hongyan, Zhang, Xujun et al.2026 · 8 citationsAccounts of chemical research. 2026;59(6):969-978
MetalloDock: Decoding Metalloprotein-Ligand Interactions via Physics-Aware Deep Learning for Metalloprotein Drug Discovery.41527511 · Zhang, Hui, Zhang, Xujun, Su, Qun et al.2026 · 7 citationsJournal of the American Chemical Society. 2026;148(3):3086-3101
Unlocking the application potential of AlphaFold3-like approaches in virtual screening.41403459 · Shen, Chao, Zhang, Xujun, Gu, Shukai et al.2025 · 16 citationsChemical science. 2025
A virtual platform for automated hybrid organic-enzymatic synthesis planning.41298428 · Wang, Xiaorui, Yin, Xiaodan, Zhang, Xujun et al.2025 · 3 citationsNature communications. 2025;16(1):10929
ECloudGen: leveraging electron clouds as a latent variable to scale up structure-based molecular design.41094041 · Zhang, Odin, Jin, Jieyu, Wu, Zhenxing et al.2025 · 7 citationsNature computational science. 2025;5(11):1017-1028
Graph Neural Networks in Modern AI-Aided Drug Discovery.40959983 · Zhang, Odin, Lin, Haitao, Zhang, Xujun et al.2025 · 91 citationsChemical reviews. 2025;125(20):10001-10103
CarsiDock-Cov: A deep learning-guided approach for automated covalent docking and screening.41311379 · Shen, Chao, Du, Hongyan, Zhang, Xujun et al.2025 · 11 citationsActa pharmaceutica Sinica. B. 2025;15(11):5758-5771
BioScore: A Foundational Scoring Function For Diverse Biomolecular Complexes2507.10877v1 · Yuchen Zhu, Jihong Chen, Yitong Li et al.2025 · 0 citationsarXiv
HawkDock version 2: an updated web server to predict and analyze the structures of protein-protein complexes.40326522 · Zhang, Xujun, Jiang, Linlong, Weng, Gaoqi et al.2025 · 46 citationsNucleic acids research. 2025;53(W1):W306-W315
ChargeNet: E(3) Equivariant Graph Attention Network for Atomic Charge Prediction.40530778 · Gou, Qiaolin, Su, Qun, Wang, Jike et al.2025 · 1 citationJournal of chemical information and modeling. 2025;65(19):10364-10374
LumiCharge: Spherical Harmonic Convolutional Networks for Atomic Charge Prediction in Drug Discovery.40521781 · Su, Qun, Zhang, Hui, Gou, Qiaolin et al.2025 · 0 citationsThe journal of physical chemistry letters. 2025;16(25):6334-6344
Token-Mol 1.0: tokenized drug design with large language models.40360500 · Wang, Jike, Qin, Rui, Wang, Mingyang et al.2025 · 26 citationsNature communications. 2025;16(1):4416
AutoLoop: a novel autoregressive deep learning method for protein loop prediction with high accuracy2505.03121v1 · Tianyue Wang, Xujun Zhang, Langcheng Wang et al.2025 · 0 citationsarXiv
Discovery of antimicrobial peptides with notable antibacterial potency by an LLM-based foundation model.40043127 · Wang, Jike, Feng, Jianwen, Kang, Yu et al.2025 · 113 citationsScience advances. 2025;11(10):eads8932
Comprehensive Evaluation of End-Point Free Energy Methods in DNA-Ligand Interaction Predictions.39888349 · Li, Cuiyu, Du, Hongyan, Zhang, Chengwei et al.2025 · 5 citationsJournal of chemical information and modeling. 2025;65(4):2014-2025
Correction: FragGen: towards 3D geometry reliable fragment-based molecular generation.39713761 · Zhang, Odin, Huang, Yufei, Chen, Shicheng et al.2025 · 0 citationsChemical science. 2025;16(3):1467
Skoda's division theorem for -optimal pairs2411.15670v2 · Zhuo Liu, Xujun Zhang2024 · 0 citationsarXiv
CovalentInDB 2.0: an updated comprehensive database for structure-based and ligand-based covalent inhibitor design and screening.39441070 · Du, Hongyan, Zhang, Xujun, Wu, Zhenxing et al.2025 · 32 citationsNucleic acids research. 2025;53(D1):D1322-D1327
FragGen: towards 3D geometry reliable fragment-based molecular generation.39568888 · Zhang, Odin, Huang, Yufei, Cheng, Shichen et al.2024 · 16 citationsChemical science. 2024;15(46):19452-19465
Enabling target-aware molecule generation to follow multi objectives with Pareto MCTS.39223327 · Yang, Yaodong, Chen, Guangyong, Li, Jinpeng et al.2024 · 11 citationsCommunications biology. 2024;7(1):1074
Highly Accurate and Efficient Deep Learning Paradigm for Full-Atom Protein Loop Modeling with KarmaLoop.39055686 · Wang, Tianyue, Zhang, Xujun, Zhang, Odin et al.2024 · 4 citationsResearch (Washington, D.C.). 2024;7:0408
Discovery of novel antimicrobial peptides with notable antibacterial potency by a LLM-based foundation model2407.12296v2 · Jike Wang, Jianwen Feng, Yu Kang et al.2024 · 0 citationsarXiv
Token-Mol 1.0: Tokenized drug design with large language model2407.07930v2 · Jike Wang, Rui Qin, Mingyang Wang et al.2024 · 2 citationsarXiv
DrugFlow: An AI-Driven One-Stop Platform for Innovative Drug Discovery.38920405 · Shen, Chao, Song, Jianfei, Hsieh, Chang-Yu et al.2024 · 51 citationsJournal of chemical information and modeling. 2024;64(14):5381-5391
Hepatitis B virus X protein promotes tumor glycolysis by downregulating lncRNA OIP5-AS1/HKDC1 in HCC.38636768 · Shi, Fan, Jiang, Jingjing, Wang, Baohua et al.2024 · 12 citationsCellular signalling. 2024;119:111183
Advancing Ligand Docking through Deep Learning: Challenges and Prospects in Virtual Screening.38577892 · Zhang, Xujun, Shen, Chao, Zhang, Haotian et al.2024 · 91 citationsAccounts of chemical research. 2024;57(10):1500-1509
Deep Geometry Handling and Fragment-wise Molecular 3D Graph Generation2404.00014v1 · Odin Zhang, Yufei Huang, Shichen Cheng et al.2024 · 3 citationsarXiv
Comprehensive Evaluation of 10 Docking Programs on a Diverse Set of Protein-Cyclic Peptide Complexes.38483249 · Zhao, Huifeng, Jiang, Dejun, Shen, Chao et al.2024 · 18 citationsJournal of chemical information and modeling. 2024;64(6):2112-2124
Harnessing deep learning for enhanced ligand docking.38160084 · Zhang, Xujun, Shen, Chao, Hsieh, Chang-Yu et al.2024 · 7 citationsTrends in pharmacological sciences. 2024;45(2):103-106
CarsiDock: a deep learning paradigm for accurate protein-ligand docking and screening based on large-scale pre-training.38274053 · Cai, Heng, Shen, Chao, Jian, Tianye et al.2024 · 77 citationsChemical science. 2024;15(4):1449-1471
Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency.38171930 · Wang, Tianyue, Wang, Langcheng, Zhang, Xujun et al.2024 · 17 citationsBriefings in bioinformatics. 2023;25(1)
A flexible data-free framework for structure-based de novo drug design with reinforcement learning.37969589 · Du, Hongyan, Jiang, Dejun, Zhang, Odin et al.2026 · 23 citationsChemical science. 2023;14(43):12166-12181
ML-PLIC: a web platform for characterizing protein-ligand interactions and developing machine learning-based scoring functions.37738401 · Zhang, Xujun, Shen, Chao, Wang, Tianyue et al.2023 · 3 citationsBriefings in bioinformatics. 2023;24(5)
Efficient and accurate large library ligand docking with KarmaDock.38177786 · Zhang, Xujun, Zhang, Odin, Shen, Chao et al.2024 · 170 citationsNature computational science. 2023;3(9):789-804
Osteopontin May Improve Postinjury Muscle Repair Via Matrix Metalloproteinases And tgf-β Activation in Regular Exercise.37575268 · Wang, Yuchong, Hong, Liang, Jiang, Jingjing et al.2023 · 17 citationsInternational journal of medical sciences. 2023;20(9):1202-1211
Delete: Deep Lead Optimization Enveloped in Protein Pocket through Unified Deleting Strategies and a Structure-aware Network2308.02172v1 · Haotian Zhang, Huifeng Zhao, Xujun Zhang et al.2023 · 4 citationsarXiv
TB-IECS: an accurate machine learning-based scoring function for virtual screening.37403155 · Zhang, Xujun, Shen, Chao, Jiang, Dejun et al.2023 · 24 citationsJournal of cheminformatics. 2023;15(1):63
A generalized protein-ligand scoring framework with balanced scoring, docking, ranking and screening powers.37538816 · Shen, Chao, Zhang, Xujun, Hsieh, Chang-Yu et al.2023 · 80 citationsChemical science. 2023;14(30):8129-8146
Topology-Based and Conformation-Based Decoys Database: An Unbiased Online Database for Training and Benchmarking Machine-Learning Scoring Functions.37317043 · Zhang, Xujun, Shen, Chao, Wang, Tianyue et al.2023 · 3 citationsJournal of medicinal chemistry. 2023;66(13):9174-9183
Molecular Generation with Reduced Labeling through Constraint Architecture.37184885 · Wang, Jike, Zeng, Yundian, Sun, Huiyong et al.2023 · 10 citationsJournal of chemical information and modeling. 2023;63(11):3319-3327
MetalProGNet: a structure-based deep graph model for metalloprotein-ligand interaction predictions.36845922 · Jiang, Dejun, Ye, Zhaofeng, Hsieh, Chang-Yu et al.2023 · 28 citationsChemical science. 2023;14(8):2054-2069
VGSC-DB: an online database of voltage-gated sodium channels.36320030 · Wang, Gaoang, Yu, Jiahui, Du, Hongyan et al.2022 · 6 citationsJournal of cheminformatics. 2022;14(1):75
Osteopontin Exacerbates High-Fat Diet-Induced Metabolic Disorders in a Microbiome-Dependent Manner.36300928 · Chen, Jianing, Zeng, Ping, Gong, Lan et al.2023 · 15 citationsmBio. 2022;13(6):e0253122
Boosting Protein-Ligand Binding Pose Prediction and Virtual Screening Based on Residue-Atom Distance Likelihood Potential and Graph Transformer.35917397 · Shen, Chao, Zhang, Xujun, Deng, Yafeng et al.2022 · 182 citationsJournal of medicinal chemistry. 2022;65(15):10691-10706
Proteome-Wide Profiling of the Covalent-Druggable Cysteines with a Structure-Based Deep Graph Learning Network.35958111 · Du, Hongyan, Jiang, Dejun, Gao, Junbo et al.2022 · 25 citationsResearch (Washington, D.C.). 2022;2022:9873564
Lamina propria interleukin 17 A aggravates natural killer T-cell activation in autoimmune hepatitis.35583908 · Chen, Jianing, Li, Xuehui, Zeng, Ping et al.2022 · 9 citationsFASEB journal : official publication of the Federation of American Societies for Experimental Biology. 2022;36(6):e22346
TocoDecoy: A New Approach to Design Unbiased Datasets for Training and Benchmarking Machine-Learning Scoring Functions.35642777 · Zhang, Xujun, Shen, Chao, Liao, Ben et al.2022 · 31 citationsJournal of medicinal chemistry. 2022;65(11):7918-7932
Knowledge-based BERT: a method to extract molecular features like computational chemists.35438145 · Wu, Zhenxing, Jiang, Dejun, Wang, Jike et al.2022 · 92 citationsBriefings in bioinformatics. 2022;23(3)
Influenza A virus NS1 protein hijacks YAP/TAZ to suppress TLR3-mediated innate immune response.35503798 · Zhang, Qiong, Zhang, Xujun, Lei, Xiaobo et al.2022 · 33 citationsPLoS pathogens. 2022;18(5):e1010505
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