IDRB: Publication

PUBLICATION

JOURNAL PAPER (*corresponding author; published cover article; PDF version of paper; ^&co-first author)

Publications of Year 2026 (click to show or hide the details)

L. Y. Zheng, Y. Liao, Y. T. Zhang, M. X. Liu, M. K. Lu, T. T. Fu, S. Y. Shi, X. N. Sun, C. B. Gu, H. C. Sun, M. J. Mou, H. B. Dai*, F. Zhu*. Measuring and locating the changes in protein structure using MELO. Nature Communications (impact factor of the publication year: 15.7, 综合一区 TOP 期刊). 17(1): 1360 (2026). PMID: 41490886.

H. C. Sun, Y. Zhou, R. Y. Jiang, Y. X. Liu, C. B. Gu, Z. Q. Pan, M. J. Mou, X. C. Lian, B. H. Chen, T. L. Niu, Y. Zhang, Y. T. Zhang, B. L. Zhang, X. N. Sun, H. Yang, X. Shen, Y. B. Dai, J. N. Deng, S. Q. Liu, Y. Zhang, M. Xiao, W. Q. Xie, Q. X. Yang, T. T. Fu*, F. Zhu*. Navigating the data processing for cytometry-based single-cell proteomics using ANPELA. Nature Protocols (impact factor of the publication year: 16.0, 生物一区 TOP 期刊). 21(3): 1235-1261 (2026). PMID: 41102581.

M. J. Mou, M. K. Lu, Z. M. Zhou, Y. L. Ren, X. Y. Yu, Z. Q. Pan, Y. Zhou, H. Yang, L. Y. Zheng, S. K. Gu, Y. Zhang, W. Hu, F. C. Li*, H. B. Dai*, F. Zhu*. Accurate identification of protein binding sites for all drug modalities using ALLSites. Advanced Science (impact factor of the publication year: 14.1, 综合一区 TOP 期刊). 13(10): e16530 (2026). PMID: 41454719.

Y. T. Zhang, Y. Zhou, H. W. Xu, W. H. Jiang, B. Li, D. Y. Lai, C. Wan, S. S. Wang, M. X. Zhao, Y. Tan, S. L. Lu, T. T. Fan, X. Liu, F. Zhu*, Y. Z. Chen*. Therapeutic target database 2026: facilitating targeted therapies and precision medicine. Nucleic Acids Research (impact factor of the publication year: 13.1, 生物一区 TOP 期刊). 54(D1): D1692-D1701 (2026). PMID: 41243978.

Z. H. Yu, Y. M. Wang, Y. T. Zhang, Y. Zhou, X. X. Hu, L. S. Shen, C. Ni, P. Xing, F. B. Huang, T. T. Fu, L. Y. Han*, J. Huang*, H. B. Dai*, F. Zhu*. PersADE: a database of personalized adverse drug events and their underlying molecular mechanisms. Nucleic Acids Research (impact factor of the publication year: 13.1, 生物一区 TOP 期刊). 54(D1): D1556-D1568 (2026). PMID: 41217945.

J. Liu, X. G. Liu, Y. S. Zhang, X. D. Li, Y. J. Sun, T. T. Li, L. F. Wei, M. J. Mou, H. Yang, P. F. Yuan, X. Li, Z. Y. Zhang, Y. H. Jia, Y. Fu, Y, T. Zhang*, Y. Zhang*, Q. Z. Jia*, F. Zhu*. RadioPharm: the database of radiopharmaceuticals (RPs). Nucleic Acids Research (impact factor of the publication year: 13.1, 生物一区 TOP 期刊). 54(D1): D1608-D1615 (2026). PMID: 41099609.

X. R. Qin, Y. P. Zhang, Y. J. Wang, Y. T. Zhang, J. C. Jing, Y. Y. Zhang, G. X. Xu, H. P. Teng, T. J. Wang, L. Fu, Y. Zhou*, X. Liu*, F. Zhu*. TPDdb: the comprehensive database of targeted protein degrader (TPD). Nucleic Acids Research (impact factor of the publication year: 13.1, 生物一区 TOP 期刊). 54(D1): D1683-D1691 (2026). PMID: 41091922.

Q. Gao, X. Y. Yu, K. X. Liu, Z. Y. Zhu, M. T. Chen, X. H. Zhao, Z. L. Liao, L. H. Xu, Y. Zhou*, F. Zhu*, X. B. Sui*. NPCDR 2.0: the activity and structure landscape of natural product-based drug combination. Nucleic Acids Research (impact factor of the publication year: 13.1, 生物一区 TOP 期刊). 54(D1): D1528-D1536 (2026). PMID: 41206750.

X. Zhang, S. N. Yang, X. B. Xu, Y. T. Lin, H. C. Sun, B. Y. Zhu, W. Y. Zhao, B. B. Zhou, Y. Lou, X. Y. Wang, S. Q. Chen, Q. J. He, F. Zhu*, Z. Zhou*. scMOVIR: a single-cell multi-omics database for human viral infections and immune responses. Nucleic Acids Research (impact factor of the publication year: 13.1, 生物一区 TOP 期刊). 54(D1): D871-D883 (2026). PMID: 41231764.

M. J. Mou, J. S. Zhang, X. G. Liu, H. Yang, T. T. Fu, H. B. Zhang, Y. M. Zhu, T. L. Niu, X. D. Li, Y. G. Ge, Z. Q. Pan, X. Y. Liu, H. C. Sun, T. Y. Zhang, Y. Zhang*, F. Zhu*, J. Q. Gao*. Unveiling the bioactive landscape of drug inactive ingredients (DIGs) using deep transfer learning. Acta Pharmaceutica Sinica B (impact factor of the publication year: 14.6, 医学一区 TOP 期刊). 16(7): 4128-414 (2026). PMID: 42453407.

Y. L. Ren, M. J. Mou*, Y. M. Zhu, Z. Q. Pan, K. Zhang, Y. T. Qian, Y. Zhang, J. L. Li, T. T. Fu*, F. Zhu*. Accurate identification of covalently ligandable cysteines using CCSite. Journal of Medicinal Chemistry (impact factor of the publication year: 7.27, 医学一区 TOP 期刊). DOI: 10.1021/acs.jmedchem.6c01911 (2026). PMID: XXXXXXXX.

Publications of Year 2025 (click to show or hide the details)

Y. Zhou, Y. T. Zhang, H. W. Xu, Z. Chen, S. J Huang, Y. H. Li, J. B. Fu, H. N. Zhang, D. H. Zhao, X. C. Lian, Y. Zhou, X. Y. Shen, K. X. Liu, Y. Q. Qiu, Y. Z. Wang, W. Q. Xie, L. Y. Han, H. B. Dai, F. Zhu*. Dynamic clinical trial success rates for drugs in the 21st century. Nature Communications (impact factor of the publication year: 15.7, 综合一区 TOP 期刊). 16(1): 9537 (2025). PMID: 41162353.

J. Y. Yin, H. Ma, Y. T. Qi, Q. W. Zhao, S. Zeng, F. C. Li*, F. Zhu*. MDIPID: Microbiota-drug interaction and disease phenotype interrelation database. iMeta (impact factor of the publication year: 33.2, 生物一区 TOP 期刊). 4(2): e70019 (2025). PMID: 40236778.

Y. X. Wang, M. J. Mou, S. J. Huang, W. Zhang, Z. Q. Pan, J. Tang, Y. H. Wang, Q. X. Yang*, F. Zhu*. Interpretation of RNA universe and coding potential using IntRNA. Advanced Science (impact factor of the publication year: 14.1, 综合一区 TOP 期刊). 12(43): e09518 (2025). PMID: 40847441.

Y. T. Zhang, X. C. Lian, H. W. Xu, S. S. Zhu, H. Zhang, Z. H. Ni, T. T. Fu, S. P. Liu, L. Tao*, Y. Zhou*, F. Zhu*. OrgXenomics: an integrated proteomic knowledge base for patient-derived organoid and xenograft. Nucleic Acids Research (impact factor of the publication year: 16.7, 生物二区 TOP 期刊). 53(D1): D504-D515 (2025). PMID: 39373514.

Y. T. Zhang, W. H. Jiang, T. Li, H. W. Xu, Y. M. Zhu, K. R. Fang, X. Y. Ren, S. S. Wang, Y. Z. Chen*, Y. Zhou*, F. Zhu*. SubCELL: the landscape of subcellular compartment-specific molecular interactions. Nucleic Acids Research (impact factor of the publication year: 16.7, 生物二区 TOP 期刊). 53(D1): D738-D747 (2025). PMID: 39373488.

X. N. Sun, H. Y. Li, Z. Chen, Y. Zhang, Z. L. Wei, H. W. Xu, Y. Liao, W. H. Jiang, Y. C. Ge, L. Y. Zheng, T. Li, Y. T. Wu, M. Y. Luo, L. Fang, X. W. Dong, M. Xiao, L. Y. Han*, Q. Z. Jia*, F. Zhu*. PDCdb: the biological activity and pharmaceutical information of peptide-drug conjugate (PDC). Nucleic Acids Research (impact factor of the publication year: 16.7, 生物二区 TOP 期刊). 53(D1): D1476-D1485 (2025). PMID: 39360619.

Y. C. Ge, M. J. Yang, X. Y. Yu, Y. Zhou, Y. T. Zhang, M. J. Mou, Z. Chen, X. N. Sun, F. Ni, T. T. Fu*, S. P. Liu*, L. Y. Han*, F. Zhu*. MolBiC: the cell-based landscape illustrating molecular bioactivities. Nucleic Acids Research (impact factor of the publication year: 16.7, 生物二区 TOP 期刊). 53(D1): D1683-D1691 (2025). PMID: 39373530.

X. Y. Shen, Y. T. Zhang, J. M. Li, Y. Zhou, S. Butensky, Y. C. Zhang, Z. W. Cai, A. T. DeWan, S. A. Khan, H. Yan, C. H. Johnson*, F. Zhu*. OncoSexome: the landscape of sex-based differences in oncologic diseases. Nucleic Acids Research (impact factor of the publication year: 16.7, 生物二区 TOP 期刊). 53(D1): D1443-D1459 (2025). PMID: 39535034.

Y. L. Li, F. C. Li, Z. X. Duan, R. H. Liu, W. T. Jiao, H. B. Wu, F. Zhu*, W. W. Xue*. SYNBIP 2.0: epitopes mapping, sequence expansion, and scaffolds discovery for synthetic binding protein innovation. Nucleic Acids Research (impact factor of the publication year: 16.7, 生物二区 TOP 期刊). 53(D1): D595-D603 (2025). PMID: 39413165.

S. S. Fu, Z. Chen, Z. M. Luo, M. Y. Nie, T. T. Fu, Y. Zhou, Q. X. Yang*, F. Zhu*, F. Ni*. Chem(Pro)2: the atlas of chemoproteomic probes labelling human proteins. Nucleic Acids Research (impact factor of the publication year: 16.7, 生物二区 TOP 期刊). 53(D1): D1651-D1662 (2025). PMID: 39436046.

M. M. Wei, J. C. Wu, S. Z. Bai, Y. X. Zhou, Y. C. Chen, X. Zhang, W. Y. Zhao, Y. Chi, G. Pan, F. Zhu*, S. Q. Chen*, Z. Zhou*. TRAIT: a comprehensive database for T-cell receptor-antigen interactions. Genomics Proteomics Bioinformatics (impact factor of the publication year: 11.5, 生物二区 TOP 期刊). 23(3): qzaf033 (2025). PMID: 40257421.

T. T. Fu, K. Zhang, T. J. Hou*, C. S. Wu*, F. Zhu*. Artificial intelligence empowering the full spectrum of drug discovery. Journal of Pharmaceutical Analysis (impact factor of the publication year: 8.9, 医学一区 TOP 期刊). 15(6): 101438 (2025). PMID: XXXXXXX.

F. Zhu*, C. S. Wu, T. J. Hou. Innovative pharmaceutical research facilitated by AI. Journal of Pharmaceutical Analysis (impact factor of the publication year: 8.9, 医学一区 TOP 期刊). 15(6): 101388 (2025). PMID: XXXXXXX.

M. J. Mou, Z. C. Zhang, Z. Q. Pan, F. Zhu*. Deep learning for predicting biomolecular binding sites of proteins. Research (impact factor of the publication year: 8.5, 综合一区 TOP 期刊). 8: 0615 (2025). PMID: 39995900.

J. Y. Yin, H. Y. Zhang, X. N. Sun, N. X. You, M. J. Mou, M. K. Lu, Z. Q. Pan, F. C. Li, H. L. Li*, S. Zeng*, F. Zhu*. Decoding drug response with structurized gridding map-based cell representation. IEEE Journal of Biomedical and Health Informatics (impact factor of the publication year: 6.7, 工程技术二区 TOP 期刊). 29(3): 1702-1713 (2025). PMID: 38090819.

J. Y. Yin, Y. T. Qi, F. Zhu*, S. Zeng*. The application of artificial intelligence in drug ADME research. Current Drug Metabolism (impact factor of the publication year: 1.8, 医学四区期刊). 26(2): 73-77 (2025). PMID: 40539355.

Y. H. Liu, H. Q. Xu, S. S. Zhu, Y. F. Hong, X. W. Li, H. X. Li, J. P. Xiong, H. Xiao, J. H. Bu, F. Zhu*, L. Tao*. ASVirus: a comprehensive knowledgebase for the viral alternative splicing. Journal of Chemical Information and Modeling (impact factor of the publication year: 5.7, 化学二区 TOP 期刊). 65(6): 2722-2729 (2025). PMID: 40063927.

T. L. Niu, Y. M. Zhu, M, J, Mou, T. T. Fu, H. Yang, H. C. Sun, Y. X. Liu, F. Zhu*, Y. Zhang*, Y. X. Liu*. Identification of natural product-based drug combination (NPDC) using artificial intelligence. Chinese Journal of Natural Medicines (impact factor of the publication year: 4.9, 医学二区期刊). 23(11): 1377-1390 (2025). PMID: 41260785.

Y. He, F. Pan, Y. T. Shan, Y. F. Pan, Y. H. Wei, Y. C. Chen, Y. H. Chen, Y. Liu, Z. Y. Zeng, Z. Zhou, F. Zhu, E. Holmes, J. P. Ye, J. Li, Y. L. Shu, M. Shi*, Z. R. Li*. Generalized biological foundation model with unified nucleic acid and protein language. Nature Machine Intelligence (impact factor of the publication year: 18.8, 计算机科学一区 TOP 期刊). 7: 942-953 (2025). PMID: N.A.

H. Y. Du, X. J. Zhang, Z. X. Wu, O. Zhang, S. K. Gu, M. Y. Wang, F. Zhu, D. Li, T. J. Hou*, P. C. Pan*. CovalentInDB 2.0: an updated comprehensive database for structure-based and ligand-based covalent inhibitor design and screening. Nucleic Acids Research (impact factor of the publication year: 16.7, 生物二区 TOP 期刊). 53(D1): D1322-D1327 (2025). PMID: 39441070.

H. F. Yu, Q. Y. Zhou, Y. X. Chen, C. X. Zhong, T. T. Fu, X. F. Xiong, F. Zhu, L. B. Wang*, Y. Sun*. Neddylation inhibitor MLN4924 enhances H3K18 lactylation via binding to LDH and downregulates ITGB4 to block metastasis. Journal of Biological Chemistry (impact factor of the publication year: 3.9, 医学二区期刊). 301(9): 110575 (2025). PMID: 40784455.

Publications of Year 2024 (click to show or hide the details)

Y. Zhou, Y. T. Zhang, D. H. Zhao, X. Y. Yu, X. Y. Shen, Y. Zhou, S. S. Wang, Y. Q. Qiu, Y. Z. Chen*, F. Zhu*. TTD: therapeutic target database describing target druggability information. Nucleic Acids Research (impact factor of the publication year: 14.9, 生物二区 TOP 期刊). 52(D1): 1465-1477 (2024). PMID: 37713619.

L. T. Shen, X. N. Sun, Z. Chen, Y. Guo, Z. Y. Shen, Y. Song, W. X. Xin, H. Y. Ding, X. Y. Ma, W. B. Xu, W. Y. Zhou, J. X. Che, L. L. Tan, L. S. Chen, S. Q. Chen, X. W. Dong*, L. Fang*, F. Zhu*. ADCdb: the database of antibody-drug conjugates. Nucleic Acids Research (impact factor of the publication year: 14.9, 生物二区 TOP 期刊). 52(D1): 1097-1109 (2024). PMID: 37831118.

Y. Zhang, H. C. Sun, W. Zhang, T. T. Fu, S. J. Huang, M. J. Mou, J. S. Zhang, J. Q. Gao, Y. C. Ge*, Q. X. Yang*, F. Zhu*. CellSTAR: a comprehensive resource for single-cell transcriptomic annotation. Nucleic Acids Research (impact factor of the publication year: 14.9, 生物二区 TOP 期刊). 52(D1): 859-870 (2024). PMID: 37855686.

X. N. Wang, Y. T. Zhang, Z. P. Li, Z. X. Duan, M. H. Guo, Z. Wang, F. Zhu*, W. W. Xue*. PROSCA: an online platform for humanized scaffold mining facilitating rational protein engineering. Nucleic Acids Research (impact factor of the publication year: 14.9, 生物二区 TOP 期刊). 52(W1): 272-279 (2024). PMID: 38738624.

Y. F. Hong, H. Q. Xu, Y. H. Liu, S. S. Zhu, C. Tian, G. X. Chen, F. Zhu*, L. Tao*. DDID: a comprehensive resource for visualization and analysis of diet-drug interactions. Briefings in Bioinformatics (impact factor of the publication year: 9.5, 生物二区 TOP 期刊). 25(3): bbae212 (2024). PMID: 38711369.

Y. Zhou, Z. Chen, M. J. Yang, F. Y. Chen, J. Y. Yin, Y. T. Zhang, X. H. Zhou, X. N. Sun, Z. H. Ni, L. Chen, Q. Lv, F. Zhu*, S. P. Liu*. FERREG: ferroptosis-based regulation of disease occurrence, progression and therapeutic response. Briefings in Bioinformatics (impact factor of the publication year: 9.5, 生物二区 TOP 期刊). 25(3): bbae223 (2024). PMID: 38742521.

X. Zhang, J. C. Wu, Y. Y. Luo, Y. L. Wang, Y. J. Wu, X. B. Xu, Y. F. Zhang, R. Y. Kong, Y. Chi, Y. S. Sun, S. Q. Chen, Q. J. He, F. Zhu*, Z. Zhou*. CovEpiAb: a comprehensive database and analysis resource for immune epitopes and antibodies of human coronaviruses. Briefings in Bioinformatics (impact factor of the publication year: 9.5, 生物二区 TOP 期刊). 25(3): bbae183 (2024). PMID: 38653491.

Y. Zhou, Y. T. Zhang, Z. C. Zhang, Z. M. Zhou, F. Zhu*. AI comes to the nobel prize and drug discovery. Journal of Pharmaceutical Analysis (impact factor of the publication year: 8.8, 医学一区期刊). 14(11): 101160 (2024). PMID: 39850961.

H. Q. Xu, H. Xiao, J. H. Bu, Y. F. Hong, Y. H. Liu, Z. Y. Tao, S. F. Ding, Y. T. Xia, E. Wu, Z. Yan, W. Zhang, G. X. Chen, F. Zhu*, L. Tao*. EMNPD: a comprehensive endophytic microorganism natural products database for prompt the discovery of new bioactive substances. Journal of Cheminformatics (impact factor of the publication year: 8.6, 化学二区期刊). 15(1): c115 (2024). PMID: 38017550.

Z. Zhang, F. C. Li, Z. X. Duan, C. Q. Shi, X. N. Wang F. Zhu*, W. W. Xue*. OPTICS: an interactive online platform for photosensory and bio-functional proteins in optogenetic systems. Computers in Biology and Medicine (impact factor of the publication year: 7.7, 工程技术二区期刊). 178: 108687 (2024). PMID: 38870722.

C. F. Xu, J. T. Huang, Y. Q. Gao, W. X. Zhao, Y. Q. Shen, F. H. Luo, G. Yu, F. Zhu*, Y. Ni*. OBMeta: a comprehensive web server to analyze and validate gut microbial features and biomarkers for obesity-associated metabolic diseases. Bioinformatics (impact factor of the publication year: 6.9, 生物二区 TOP 期刊). 39(12): btad715 (2023). PMID: 38078817.

X. D. Li, C. Z. Wang, X. Chai, X. G. Liu, K. N. Qiao, Y. Fu, Y. Z. Jin, Q. Z. Jia*, F. Zhu*, Y. Zhang*. Discovery of potent selective HDAC6 inhibitors with 5-phenyl-1H-indole fragment: virtual screening, rational design, and biological evaluation. Journal of Chemical Information and Modeling (impact factor of the publication year: 5.6, 化学二区 TOP 期刊). 64(15): 6147-6161 (2024). PMID: 39042494.

K. M. Merz*, Y. S. Choong*, G. W. Wei*, F. Zhu*. Editorial cutting-edge methodologies in omics data analysis. Journal of Chemical Information and Modeling (impact factor of the publication year: 5.6, 化学二区 TOP 期刊). 64(13): 4939-4940 (2024). PMID: 38973305.

K. M. Merz*, Y. S. Choong*, Z. Cournia*, O. Isayev*, T. A. Soares*, G. W. Wei*, F. Zhu*. Editorial machine learning in materials science. Journal of Chemical Information and Modeling (impact factor of the publication year: 5.6, 化学二区 TOP 期刊). 64(10): 3959-3960 (2024). PMID: 38798192.

K. M. Merz*, G. W. Wei*, F. Zhu*. Editorial machine learning in bio-cheminformatics. Journal of Chemical Information and Modeling (impact factor of the publication year: 5.6, 化学二区 TOP 期刊). 64(7): 2125-2128 (2024). PMID: 38587006.

Y. L. Li, W. T. Jiao, R. H. Liu, X. J. Deng, F. Zhu*, W. W. Xue*. Expanding the sequence spaces of synthetic binding protein using deep learning-based framework ProteinMPNN. Frontiers of Computer Science (impact factor of the publication year: 5.6, 计算机三区期刊). 19(5): 195903 (2024). PMID: N.A.

H. Li, H. Seada, S. Madnick, H. Zhao, Z. Z. Chen, F. C. Li, F. Zhu, S. Hall, K. Boekelheide*. Machine learning-assisted high-content imaging analysis of 3D MCF7 microtissues for estrogenic effect prediction. Scientific Reports (impact factor of the publication year: 4.6, 化学二区期刊). 14(1): 2999 (2024). PMID: 38316851.

Publications before Year 2024 (click to show or hide the details)

M. K. Lu, J. Y. Yin, Q. Zhu, G. L. Lin, M. J. Mou, F. Y. Liu, Z. Q. Pan, N. X. You, X. C. Lian, F. C. Li, H. N. Zhang, L. Y. Zheng, W. Zhang, H. Y. Zhang, Z. H. Shen, Z. Gu, H. L. Li*, F. Zhu*. Artificial intelligence in pharmaceutical sciences. Engineering (impact factor of the publication year: 12.8, 工程技术一区 TOP 期刊). 27: 37-69 (2023). PMID: N.A.

K. M. Merz, G. W. Wei, F. Zhu*. Editorial harnessing the power of large language model-based chatbots for scientific discovery. Journal of Chemical Information and Modeling (impact factor of the publication year: 6.2, 化学二区 TOP 期刊). 63(17): 5395 (2023). PMID: 37691490.

W. Hu, W. Zhang, Y. Zhou, Y. C. Luo, X. N. Sun, H. M. Xu, S. Y. Shi, T. Li, Y. C. Xu, Q. Q. Yang, Y. Q. Qiu, F. Zhu*, H. B. Dai*. MecDDI: clarified drug-drug interaction mechanism facilitating rational drug use and potential drug-drug interaction prediction. Journal of Chemical Information and Modeling (impact factor of the publication year: 6.2, 化学二区 TOP 期刊). 63(5): 1626-1636 (2023). PMID: PMID: 36802582.

K. M. Merz, G. W. Wei, F. Zhu*. Editorial machine learning in bio-cheminformatics. Journal of Chemical Information and Modeling (impact factor of the publication year: 6.2, 化学二区 TOP 期刊). 63(1): 1 (2023). PMID: 36617996.

J. B. Fu, F. Zhu, C. J. Xu, Y. Li*. Metabolomics meets systems immunology. EMBO Reports (impact factor of the publication year: 9.0, 生物二区期刊). 24(4): e55747 (2023). PMID: 36916532.

Q. Ye, R. L. Xu, D. Li, Y. Kang, Y. F. Deng, F. Zhu, J. M. Chen*, S. B. He, C. Y. Hsieh*, T. J. Hou*. Integrating multi-modal deep learning on knowledge graph for the discovery of synergistic drug combinations against infectious diseases. Cell Reports Physical Science (impact factor of the publication year: 8.9, 综合二区期刊). 4(8): 101520 (2023). PMID: N.A.

S. Z. Deng, H. W. Zhang*, R. P. Gou, D. Luo, Z. R. Liu, F. Zhu, W. W. Xue*. Structure-based discovery of a novel allosteric inhibitor against human dopamine transporter. Journal of Chemical Informatisson and Modeling (impact factor of the publication year: 6.2, 化学二区 TOP 期刊). 63(14): 4458-4467 (2023). PMID: 37410882.

L. D. Wang, X. Liang, H. Chen, L. J. Cao, L. Liu, F. Zhu, Y. B. Ding*, J. Tang*, Y. L. Xie*. CDEMI: characterizing differences in microbial composition and function in microbiome data. Computational and Structural Biotechnology Journal (impact factor of the publication year: 6.2, 生物二区期刊). 21: 2502-2513 (2023). PMID: 37090432.

Y. Zhou, Y. T. Zhang, X. C. Lian, F. C. Li, C. X. Wang, F. Zhu*, Y. Q. Qiu*, Y. Z. Chen*. Therapeutic target database update 2022: facilitating drug discovery with enriched comparative data of targeted agents. Nucleic Acids Research (impact factor of the publication year: 19.2, 生物一区 TOP 期刊). 50(D1): 1398-1407 (2022). PMID: 34718717.

ESI Highly Cited Paper:

The Percentile in Subject Area shown in InCites™ was 0.35% in 2023.

Media Coverage & News Report:

Chinese ZhiHu. Oct 32th, 2021.

Deep Singularity. Nov 1th, 2021.

DrugAI. Oct 30th, 2021.

X. N. Sun, Y. T. Zhang, Y. Zhou, X. C. Lian, L. L. Yan, T. Pan, T. Jin, H. Xie, Z. M. Liang, W. Q. Qiu, J. X. Wang, Z. R. Li, F. Zhu*, X. B. Sui*. NPCDR: natural product-based drug combination and its disease-specific molecular regulation. Nucleic Acids Research (impact factor of the publication year: 19.2, 生物一区 TOP 期刊). 50(D1): 1324-1333 (2022). PMID: 34664659.

C. Y. Zhang, M. J. Mou, Y. Zhou, W. Zhang, X. C. Lian, S. Y. Shi, M. K. Lu, H. C. Sun, F. C. Li, Y. X. Wang, Z. Y. Zeng, Z. R. Li, B. Zhang, Y. Q. Qiu, F. Zhu*, J. Q. Gao*. Biological activities of drug inactive ingredients (DIGs). Briefings in Bioinformatics (impact factor of the publication year: 13.9, 生物一区 TOP 期刊). 23(5): bbac160 (2022). PMID: 35524477.

L. D. Wang, W. Zhang, X. L. Wu, X. Liao, L. J. Cao, J. C. Zhai, Y. Y. Yang, Q. X. Chen, H. Q. Liu, J. Zhang, Y. B. Ding*, F. Zhu*, J. Tang*. MIAOME: human microbiome affect the host epigenome. Computational and Structural Biotechnology Journal (impact factor of the publication year: 6.2, 生物二区期刊). 20: 2455-2463 (2022). PMID: 35664224.

J. P. Pang, X. P. Hu, Y. X. Wang, J. N. Liao, X. Chai, X. W. Wang, C. Shen, J. J. Wang, L. L. Zhang, X. Y. Wang, F. Zhu, Q. J. Weng, L. Xu, T. J. Hou, D. Li*. Discovery of a novel nonsteroidal selective glucocorticoid receptor modulator by virtual screening and bioassays. Acta Pharmacologica Sinica (impact factor of the publication year: 8.2, 医学一区 TOP 期刊). 43(9): 2429-2438 (2022). PMID: 35110698.

J. P. Pang, C. Shen, W. F. Zhou, Y. X. Wang, L. H. Shan, X. Chai, Y. Shao, X. P. Hu, F. Zhu, D. Y. Zou, L. Xiao, L. Xu, X. H. Xu, D. Li*, T. J. Hou*. Discovery of novel antagonists targeting the DNA binding domain of androgen receptor by integrated docking-based virtual screening and bioassays. Acta Pharmacologica Sinica (impact factor of the publication year: 8.2, 医学一区 TOP 期刊). 43(1): 229-239 (2022). PMID: 33767381.

H. C. Zhao, S. K. Wang, K. Zheng, Q. C. Zhao, F. Zhu, J. X. Wang*. A similarity-based deep learning approach for determining the frequencies of drug side effects. Briefings in Bioinformatics (impact factor of the publication year: 13.9, 生物一区 TOP 期刊). 23(1): bbab449 (2022). PMID: 34718402.

G. W. Wei, F. Zhu, K. M. Merz*. Editorial on machine learning. Journal of Chemical Information and Modeling (impact factor of the publication year: 6.2, 化学二区 TOP 期刊). 62(17): 3941 (2022). PMID: 36044023.

G. W. Wei*, T. A. Soares, H. Wahab, F. Zhu. Computational chemistry in Asia. Journal of Chemical Information and Modeling (impact factor of the publication year: 6.2, 化学二区 TOP 期刊). 62(21): 5035-5037 (2022). PMID: 36373284.

Y. H. Wang, J. C. Zhai, X. L. Wu, E. A. Adu-Gyamfi, L. P. Yang, T. H. Liu, M. J. Wang, Y. B. Ding, F. Zhu, Y. X. Wang*, J. Tang*. LncRNA functional annotation with improved false discovery rate achieved by disease associations. Computational and Structural Biotechnology Journal (impact factor of the publication year: 6.2, 生物二区期刊). 20: 322-332 (2022). PMID: 35035785.

W. X. Shen, X. Zeng, F. Zhu, Y. L. Wang, C. Qin, Y. Tan, Y. Y. Jiang*, Y. Z. Chen*. Out-of-the-box deep learning prediction of pharmaceutical properties by broadly learned knowledge-based molecular representations. Nature Machine Intelligence (impact factor of the publication year: 15.5, 综合一区 TOP 期刊). 3: 334-343 (2021). PMID: N.A.

S. Y. Chen, S. Y. Yang, X. Zeng, F. Zhu, Y. Tan, Y. Y. Jiang*, Y. Z. Chen*. Combining kinase inhibitors for optimally co-targeting cancer and drug escape by exploitation of drug target promiscuities. Drug Development Research (impact factor of the publication year: 4.4, 医学四区期刊). 82(1): 133-142 (2021). PMID: 32931039.

Z. J. Han, W. W. Xue, L. Tao, Y. Lou, Y. Q. Qiu*, F. Zhu*. Genome-wide identification and analysis of the eQTL lncRNAs in multiple sclerosis based on RNA-seq data. Briefings in Bioinformatics (impact factor of the publication year: 11.6, 生物一区 TOP 期刊). 21(3): 1023-1037 (2020). PMID: 31323688.

ESI Highly Cited Paper:

The Percentile in Subject Area shown in InCites™ was 2.22% in 2022.

C. Shen, Z. Wang, X. J. Yao, T. L. Lei, E. C. Wang, Z. Y. Tian, F. Zhu, D. Li, T. J. Hou*. Comprehensive assessment of nine docking programs on type II kinase inhibitors: prediction accuracy of sampling power, scoring power and screening power. Briefings in Bioinformatics (impact factor of the publication year: 11.6, 生物一区 TOP 期刊). 21(1): 282-297 (2020). PMID: 30379986.

X. Ding, K. X. Fan, J. T. Hu, Z. L. Zang, S. L. Zhang, Y. Zhang, Z. C. Lin, X. D. Pei, X. Zheng, F. Zhu, H. Yang*, S. Li*. SCP2-mediated cholesterol membrane trafficking promotes the growth of pituitary adenomas via Hedgehog signaling activation. Journal of Experimental & Clinical Cancer Research (impact factor of the publication year: 5.6, 医学二区期刊). 38(1): 404 (2019). PMID: 31519191.

G. Q. Weng, E. C. Wang, Z. Wang, H. Liu, F. Zhu, D. Li, T. J. Hou*. HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA. Nucleic Acids Research (impact factor of the publication year: 11.6, 生物一区 TOP 期刊). 47(W1): 322-330 (2019). PMID: 31106357.

ESI Highly Cited Paper:

The Percentile in Subject Area shown in InCites™ was 0.53% in 2023.

Z. Wang, X. W. Wang, Y. Y. Li, T. L. Lei, E. C. Wang, D. Li, Y. Kang, F. Zhu, T. J. Hou*. farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods. Bioinformatics (impact factor of the publication year: 5.5, 生物二区 TOP 期刊). 35(10): 1777-1779 (2019). PMID: 30329012.

H. Y. Chen, W. T. Fu, Z. Wang, X. W. Wang, T. L. Lei, F. Zhu, D. Li, S. Chang, L. Xu, T. J. Hou*. Reliability of docking-based virtual screening for GPCR ligands with homology modeled structures: a case study of angiotensin II type I receptor. ACS Chemical Neuroscience (impact factor of the publication year: 4.2, 化学二区 TOP 期刊). 10(1): 677-689 (2019). PMID: 30265513.

T. L. Xie, J. Yu, W. T. Fu, Z. Wang, L. Xu, S. Chang, E. C. Wang, F. Zhu, S. Zeng, Y. Kang, T. J. Hou*. Insight into the selective binding mechanism of DNMT1 and DNMT3A inhibitors: a molecular simulation study. Physical Chemistry Chemical Physics (impact factor of the publication year: 4.1, 化学二区 TOP 期刊). 21(24): 12931-12947 (2019). PMID: 31165133.

E. C. Wang, G. Q. Weng, H. Y. Sun, H. Y. Du, F. Zhu, F. Chen, Z. Wang, T. J. Hou*. Assessing the performance of the MM/PBSA and MM/GBSA methods. 10. Impacts of enhanced sampling and variable dielectric model on protein-protein interactions. Physical Chemistry Chemical Physics (impact factor of the publication year: 4.1, 化学二区 TOP 期刊). 21(35): 18958-18969 (2019). PMID: 31453590.

P. C. Pan, J. Chen, X. J. Li, M. Y. Li, H. D. Yu, J. Zhao, J. Ni, X. W. Wang, H. Y. Sun, S. Tian, F. Zhu, F. Liu, Y. Huang, T. J. Hou*. Structure-based drug design and identification of H2O-soluble and low toxic hexacyclic camptothecin derivatives with improved efficacy in cancer and lethal inflammation models in vivo. Journal of Medicinal Chemistry (impact factor of the publication year: 6.3, 医学二区 TOP 期刊). 61(19): 8613-8624 (2018). PMID: 30227711.

F. Chen, H. Y. Sun, J. M. Wang, F. Zhu, H. Liu, Z. Wang, T. L. Lei, Y. Y. Li, T. J. Hou*. Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein-RNA complexes. RNA (impact factor of the publication year: 4.6, 生物二区期刊). 24(9): 1183-1194 (2018). PMID: 29930024.

J. Shang, B. Hu, J. M. Wang, F. Zhu, Y. Kang, D. Li, H. Y. Sun, D. X. Kong, T. J. Hou*. Cheminformatic insight into the differences between terrestrial and marine originated natural products. Journal of Chemical Information and Modeling (impact factor of the publication year: 3.8, 化学二区 TOP 期刊). 58(6): 1182-1193 (2018). PMID: 29792805.

H. Y. Sun, F. Chen, H. Liu, Z. Wang, P. C. Chen, F. Zhu, T. J. Hou*. Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches. Physical Chemistry Chemical Physics (impact factor of the publication year: 4.1, 化学二区 TOP 期刊). 20(21): 14450-14460 (2018). PMID: 29785435.

ESI Highly Cited Paper:

The Percentile in Subject Area shown in InCites™ was 0.18% in 2023.

X. T. Kong, H. Y. Sun, P. C. Pan, F. Zhu, S. Chang, L. Xu, Y. Y. Li, T. J. Hou*. Importance of protein flexibility on molecular recognition: a case study on type-I1/2 inhibitors of ALK. Physical Chemistry Chemical Physics (impact factor of the publication year: 4.1, 化学二区 TOP 期刊). 20(7): 4851-4863 (2018). PMID: 29383359.

P. C. Pan, H. D. Yu, Q. L. Liu, X. T. Kong, H. Chen, J. A. Chen, Q. Liu, D. Li, Y. Kang, H. Y. Sun, W. F. Zhou, S. Tian, S. L. Cui, F. Zhu, Y. Y. Li, Y. Huang, T. J. Hou*. Combating drug-resistant mutants of ALK with potent and selective type-I1/2 inhibitors by stabilizing unique DFG-shifted loop conformation. ACS Central Science (impact factor of the publication year: 7.9, 化学一区 TOP 期刊). 3(11): 1208-1220 (2017). PMID: 29202023.

T. Feng, F. Chen, Y. Kang, H. Y. Sun, H. Liu, D. Li, F. Zhu, T. J. Hou*. HawkRank: a new scoring function for protein-protein docking based on weighted energy terms. Journal of Cheminformatics (impact factor of the publication year: 4.2, 化学二区 TOP 期刊). 9(1): 66 (2017). PMID: 29282565.

T. L. Lei, H. Y. Sun, Y. Kang, F. Zhu, H. Liu, W. F. Zhou, Z. Wang, D. Li, Y. Y. Li, T. J. Hou*. ADMET evaluation in drug discovery. 18. Reliable prediction of chemical-induced urinary tract toxicity by boosting machine learning approaches. Molecular Pharmaceutics (impact factor of the publication year: 4.4, 医学二区期刊). 14(11): 3935-3953 (2017). PMID: 29037046.

S. Tian, X. Wang, L. L. Li, X. H. Zhang, Y. Y. Li, F. Zhu, T. J. Hou*, X. C. Zhen*. Discovery of novel and selective adenosine A2A receptor antagonists for treating parkinson's disease through comparative structure-based virtual screening. Journal of Chemical Information and Modeling (impact factor of the publication year: 3.8, 化学二区 TOP 期刊). 57(6): 1474-1487 (2017). PMID: 28463561.

X. T. Kong, H. Y. Sun, P. C. Pan, D. Li, F. Zhu, S. Chang, L. Xu, Y. Y. Li*, T. J. Hou*. How does the L884P mutation confer resistance to type-II inhibitors of JAK2 kinase: a comprehensive molecular modeling study. Scientific Reports (impact factor of the publication year: 4.3, 综合性三区期刊). 7(1): 9088 (2017). PMID: 28831147.

J. Y. An, X. D. Pei, Z. L. Zang, Z. Zhou, J. T. Hu, X. Zheng, Y. Zhang, J. J. He, L. Duan, R. F. Shen, W. H. Zhang, F. Zhu, S. Li*, H. Yang*. Metformin inhibits proliferation and growth hormone secretion of GH3 pituitary adenoma cells. Oncotarget (impact factor of the publication year: 5.2, 医学二区期刊). 8(23): 37538-37549 (2017). PMID: 28380462.

P. Zhang, L. Tao, X. Zeng, C. Qin, S. Y. Chen, F. Zhu, Z. R. Li, Y. Y. Jiang, W. P. Chen, Y. Z. Chen*. A protein network descriptor server and its use in studying protein, disease, metabolic and drug targeted networks. Briefings in Bioinformatics (impact factor of the publication year: 8.4, 生物一区 TOP 期刊). 18(6): 1057-1070 (2017). PMID: 27542402.

P. Zhang, L. Tao, X. Zeng, C. Qin, S. Y. Chen, F. Zhu, S. Y. Yang, Z. R. Li, W. P. Chen, Y. Z. Chen*. PROFEAT update: a protein features web-server with added facility to compute network descriptors for studying omics-derived networks. Journal of Molecular Biology (impact factor of the publication year: 4.6, 生物二区 TOP 期刊). 429(3): 416-425 (2017). PMID: 27742592.

H. Yang, C. Qin, Y. H. Li, L. Tao, J. Zhou, C. Y. Yu, F. Xu, Z. Chen, F. Zhu*, Y. Z. Chen*. Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information. Nucleic Acids Research (impact factor of the publication year: 9.2, 生物一区 TOP 期刊). 44(D1): 1069-1074 (2016). PMID: 26578601.

ESI Highly Cited Paper:

The Percentile in Subject Area shown in InCites™ was 0.99% in 2023.

The Percentile in Subject Area shown in InCites™ was 0.99% in 2022.

The Percentile in Subject Area shown in InCites™ was 0.69% in 2021.

The Percentile in Subject Area shown in InCites™ was 0.78% in 2020.

The Percentile in Subject Area shown in InCites™ was 0.66% in 2019.

The Percentile in Subject Area shown in InCites™ was 0.71% in 2018.

The Percentile in Subject Area shown in InCites™ was 0.87% in 2017.

G. X. Zheng, W. W. Xue*, P. P. Wang, F. Y. Yang, B. Li, X. F. Li, Y. H. Li, X. J. Yao, F. Zhu*. Exploring the inhibitory mechanism of approved selective norepinephrine reuptake inhibitors and reboxetine enantiomers by molecular dynamics study. Scientific Reports (impact factor of the publication year: 5.2, 综合性二区期刊). 6: 26883 (2016). PMID: 27230580.

Y. H. Li, P. P. Wang, X. X. Li, C. Y. Yu, H. Yang, J. Zhou, W. W. Xue, J. Tan, F. Zhu*. The human kinome targeted by FDA approved multi-target drugs and combination products: a comparative study from the drug-target interaction network perspective. PLoS ONE (impact factor of the publication year: 3.2, 生物三区期刊). 11(11): e0165737 (2016). PMID: 27828998.

X. Zheng, S. Li, Z. L. Zang, J. T. Hu, J. Y. An, X. D. Pei, F. Zhu, W. H. Zhang*, H. Yang*. Evidence for possible role of toll-like receptor 3 mediating virus-induced progression of pituitary adenomas. Molecular and Cellular Endocrinology (impact factor of the publication year: 3.8, 医学二区期刊). 426: 22-32 (2016). PMID: 26891958.

L. Tao^&, F. Zhu^&, F. Xu, Z. Chen, Y. Y. Jiang*, Y. Z. Chen*. Co-targeting cancer drug escape pathways confers clinical advantage for multi-target anticancer drugs. Pharmacological Research (impact factor of the publication year: 4.8, 医学二区期刊). 102: 123-131 (2015). PMID: 26438971.

L. Tao, P. Zhang, C. Qin, S. Y. Chen, C. Zhang, Z. Chen, F. Zhu, S. Y. Yang, Y. Q. Wei, Y. Z. Chen*. Recent progresses in the exploration of machine learning methods as in-silico ADME prediction tools. Advanced Drug Delivery Reviews (impact factor of the publication year: 15.6, 医学一区 TOP 期刊). 86: 83-100 (2015). PMID: 26037068.

L. Tao, F. Zhu, C. Qin, C. Zhang, S. Y. Chen, P. Zhang, C. L. Zhang, C. Y. Tan, C. M. Gao, Z. Chen, Y. Y. Jiang*, Y. Z. Chen*. Clustered distribution of natural product leads of drugs in the chemical space as influenced by the privileged target-sites. Scientific Reports (impact factor of the publication year: 5.6, 综合性二区期刊). 5: 9325 (2015). PMID: 25790752.

L. Tao, F. Zhu, C. Qin, C. Zhang, F. Xu, C. Y. Tan, Y. Y. Jiang*, Y. Z. Chen*. Nature's contribution to today's pharmacopeia. Nature Biotechnology (impact factor of the publication year: 32.4, 工程技术一区 TOP 期刊). 32(10): 979-980 (2014). PMID: 25299914.

C. Zhang, C. Qin, L. Tao, F. Zhu, S. Y. Chen, P. Zhang, S. Y. Yang, Y. Q. Wei, Y. Z. Chen*. A resource for facilitating the development of tools in the education and implementation of genomics-informed personalized medicine. Clinical Pharmacology & Therapeutics (impact factor of the publication year: 7.4, 医学一区 TOP 期刊). 95(6): 590-591 (2014). PMID: 24556782.

C. Qin, C. Zhang, F. Zhu, F. Xu, S. Y. Chen, P. Zhang, Y. H. Li, S. Y. Yang, Y. Q. Wei, L. Tao*, Y. Z. Chen*. Therapeutic target database update 2014: a resource for targeted therapeutics. Nucleic Acids Research (impact factor of the publication year: 8.3, 生物一区 TOP 期刊). 42(D1): 1118-1123 (2014). PMID: 24265219.

ESI Highly Cited Paper:

The Percentile in Subject Area shown in InCites™ was 2.92% in 2018.

The Percentile in Subject Area shown in InCites™ was 1.16% in 2017.

X. Liu, F. Zhu, X. H. Ma, Z. Shi, S. Y. Yang, Y. Q. Wei, Y. Z. Chen*. Predicting targeted polypharmacology for drug repositioning and multi-target drug discovery. Current Medicinal Chemistry (impact factor of the publication year: 4.9, 医学二区期刊). 20(13): 1646-1661 (2013). PMID: 23410165.

X. H. Ma, F. Zhu, X. Liu, Z. Shi, J. X. Zhang, S. Y. Yang, Y. Q. Wei, Y. Z. Chen*. Virtual screening methods as tools for drug lead discovery from large chemical libraries. Current Medicinal Chemistry (impact factor of the publication year: 4.6, 医学二区期刊). 19(32): 5562-5571 (2012). PMID: 23016548.

J. X. Zhang, J. Jia, F. Zhu, X. H. Ma, B. C. Han, X. N. Wei, C. Y. Tan, Y. Y. Jiang*, Y. Z. Chen*. Analysis of bypass signaling in EGFR pathway and profiling of bypass genes for predicting response to anticancer EGFR tyrosine kinase inhibitors. Molecular BioSystems (impact factor of the publication year: 3.8, 生物三区期刊). 8(10): 2645-2656 (2012). PMID: 22833077.

H. B. Rao^&, F. Zhu^&, G. B. Yang, Z. R. Li*, Y. Z. Chen. Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence. Nucleic Acids Research (impact factor of the publication year: 7.8, 生物一区 TOP 期刊). 39(W1): 385-390 (2011). PMID: 21609959.

X. Liu, F. Zhu, X. H. Ma, L. Tao, J. X. Zhang, S. Y. Yang, Y. Q. Wei, Y. Z. Chen*. The therapeutic target database: an internet resource for the primary targets of approved, clinical trial and experimental drugs. Expert Opinion on Therapeutic Targets (impact factor of the publication year: 3.7, 生物二区期刊). 15(8): 903-912 (2011). PMID: 21619487.

J. Jia, F. Zhu, X. H. Ma, Z. W. Cao, Y. X. Li, Y. Z. Chen*. Mechanisms of drug combinations: interaction and network perspectives. Nature Reviews Drug Discovery (impact factor of the publication year: 23.3, 医学一区 TOP 期刊). 8(2): 111-128 (2009). PMID: 19180105.

ESI Highly Cited Paper:

The Percentile in Subject Area shown in InCites™ was 0.73% in 2023.

The Percentile in Subject Area shown in InCites™ was 0.76% in 2022.

The Percentile in Subject Area shown in InCites™ was 0.91% in 2021.

The Percentile in Subject Area shown in InCites™ was 0.97% in 2020.

The Percentile in Subject Area shown in InCites™ was 1.06% in 2019.

The Percentile in Subject Area shown in InCites™ was 1.13% in 2018.

The Percentile in Subject Area shown in InCites™ was 1.39% in 2017.

X. H. Ma, J. Jia, F. Zhu, Y. Xue, Z. R. Li, Y. Z. Chen*. Comparative analysis of machine learning methods in ligand-based virtual screening of large compound libraries. Combinatorial Chemistry & High Throughput Screening (impact factor of the publication year: 2.3, 化学四区期刊). 12(4): 344-357 (2009). PMID: 19442064.

L. Y. Han, X. H. Ma, H. H. Lin, J. Jia, F. Zhu, Y. Xue, Z. R. Li, Z. W. Cao, Z. L. Ji, Y. Z. Chen*. A support vector machines approach for virtual screening of active compounds of single and multiple mechanisms from large libraries at an improved hit-rate and enrichment factor. Journal of Molecular Graphics & Modelling (impact factor of the publication year: 2.4, 生物四区期刊). 26(8): 1276-1286 (2008). PMID: 18218332.

L. Y. Han, C. J. Zheng, B. Xie, J. Jia, X. H. Ma, F. Zhu, H. H. Lin, X. Chen, Y. Z. Chen*. Support vector machines approach for predicting druggable proteins: recent progress in its exploration and investigation of its usefulness. Drug Discovery Today (impact factor of the publication year: 7.8, 药学一区 TOP 期刊). 12(7-8): 304-313 (2007). PMID: 17395090.

H. H. Lin, L. Y. Han, C. W. Yap, Y. Xue, X. H. Liu, F. Zhu, Y. Z. Chen*. Prediction of factor Xa inhibitors by machine learning methods. Journal of Molecular Graphics & Modelling (impact factor of the publication year: 2.3, 生物四区期刊). 26(2): 505-518 (2007). PMID: 17418603.

INTERNATIONAL AND DOMESTIC CONFERENCES ( news in photo)

Hosted Conference and Symposium (click to show or hide the details)

F. Zhu is the Chair of the Organizing Committee for The 4th Worldwide Chinese Computational Biology Conference. Zhejiang University, Hangzhou, P. R. China (2022).

F. Zhu is the Member of the Academic Committee for The 4th Worldwide Chinese Computational Biology Conference. Zhejiang University, Hangzhou, P. R. China (2022).

F. Zhu is the Chair of the Organizing Committee for The 11st Asia Hub for e-Drug Discovery. Zhejiang University, Hangzhou, P. R. China (2021).

F. Zhu is the Member of the Academic Committee for The 11st Asia Hub for e-Drug Discovery. Zhejiang University, Hangzhou, P. R. China (2021).

F. Zhu is the Chairman of the Symposium II (chemometrics and life science) for The 16th National Symposium of Computer & Computational Chemistry. Jilin University, Changchun, P. R. China (2021).

F. Zhu is the Member of the Academic Committee for The 16th National Symposium of Computer & Computational Chemistry. Jilin University, Changchun, P. R. China (2021).

F. Zhu is the Chairman of the Symposium IV (precision drug design and precision medicine) for The 15th National Symposium of Computer & Computational Chemistry. Fudan University, Shanghai, P. R. China (2019).

F. Zhu is the Member of the Academic Committee for The 15th National Symposium of Computer & Computational Chemistry. Fudan University, Shanghai, P. R. China (2019).

F. Zhu is the Chairman of the Symposium II (OMIC big data and medical application) for The Fourth CCF Bioinformatics Conference. South China University of Technology, Guangzhou, P. R. China (2019).

F. Zhu is the Member of the Academic Committee for The Fourth CCF Bioinformatics Conference. South China University of Technology, Guangzhou, P. R. China (2019).

F. Zhu is the Vice-chairman of the Symposium 24 Session-4 for The 31st Academic Annual Conference of the Chinese Chemical Society. Zhejiang University, Hangzhou, P. R. China (2018).

F. Zhu is the Chairman of the Symposium IV Session -7 for Asian Federation for Pharmaceutical Sciences Conference 2017. Xiamen University, Xiamen, P. R. China (2017).

F. Zhu is the Member of the Academic Committee for The 14th National Symposium of Computer & Computational Chemistry. Nanjing University, Nanjing, P. R. China (2017).

F. Zhu is the Member of the Academic Committee for The Second CCF Bioinformatics Conference (CBC-2017). Central South University, Changsha, P. R. China (2017).

F. Zhu is the Chairman of the sub-conference 103 (multi-target and protein-protein interaction) for BIT’s 6th Annual International Congress of Medichem-2016 (ICM-2016). China Pharmaceutical University, Nanjing, P. R. China (2016).

F. Zhu is the Vice-chairman of the 6th theme (study on drug transporter and PK/PD) for BIT’s 6th Annual International Congress of Medichem-2016 (ICM-2016). China Pharmaceutical University, Nanjing, P. R. China (2016)

F. Zhu is the Chair of the Organizing Committee for The 2nd Symposium on Bioinformatics and Drug Design. Chongqing University, Chongqing, P. R. China (2016).

F. Zhu is the Member of the Academic Committee for The 2nd Symposium on Bioinformatics and Drug Design. Chongqing University, Chongqing, P. R. China (2016).

F. Zhu is the Member of the Academic Committee for The 13th National Symposium of Computer & Computational Chemistry. Sun Yat-sen University, Guangzhou, P. R. China (2015).

F. Zhu is the Member of the Organizing Committee for International Symposium on Natural Product Synthesis and Innovative Process Methods for Drug Manufacture. Chongqing University, Chongqing, P. R. China (2012).

Keynote Speaker of International/Domestic Conference (click to show or hide the details)

F. Zhu*. Artificial intelligence-based discovery of new drug target. Invited keynote speaker of domestic conference for Strategy Seminar on Chemistry Division of the National Natural Science Foundation of China & 2021 Annual National Computational Toxicology Conference of China. Yanan University, Yanan, P. R. China (2021).

F. Zhu*. Promising target discovery based on multi-omics data. Invited keynote speaker of domestic conference for 2020 Annual Conference of Digitization in Medical Administration and Artificial Intelligence in Drug Discovery. Zhejiang Medical Association, Hangzhou, P. R. China (2020).

F. Zhu*. Processing of metabolomic data using NOREVA. Invited keynote speaker of domestic conference for 2020 Annal Symposium on Translational Medicine, Bioinformatics and Genomics/Proteomics/Metabolomics-based Technology. Chongqing Medical University, Chongqing, P. R. China (2020).

F. Zhu*. Therapeutic target discovery based on artificial intelligence. Invited keynote speaker of domestic conference for 2019 Forum of Intelligent Development of Traditional Chinese Medicine. China Information Association of Traditional Chinese Medicine, Shanghai, P. R. China (2019).

F. Zhu*. Clinical target discovery inspired from artificial intelligence. Invited keynote speaker of domestic conference for 1st West Lake Clinical Research and Evaluation Conference. The First Affiliated Hospital, Zhejiang University, Hangzhou, P. R. China (2018).

F. Zhu*. Identification of key factors indicating the progression timelines of novel drug targets. Invited keynote speaker of international conference for 11th China-Japan Symposium on Molecular Drug Design and Development. Zhejiang University and Chinese Academy of Medical Sciences & Peking Union Medical College, Shaoxing, P. R. China (2018).

F. Zhu*. Identification of next generation innovative therapeutic target from OMICs data. Invited keynote speaker of domestic conference for 2017 Symposium on Pharmaceutical Chemistry of the Yangtze River Delta Metropolitan Region. Hefei Institute of Physical Science, Chinese Academy of Sciences, Hefei, P. R. China (2017).

Invited Speaker of International/Domestic Conference (click to show or hide the details)

F. Zhu*. Progression-speed differentiating features of the innovative targets of first-in-class drugs. Invited speaker of international conference for The PacifiChem 2021 Symposium. International Chemical Congress of Pacific Basin Societies, Hawaii, USA (2021).

F. Zhu*. Artificial intelligence and molecular simulation for accelerating target discovery. Invited speaker of international conference for The AHeDD2019/IPAB2019 Joint Symposium. Tokyo Institute of Technology, Kawasaki, Japan (2019).

F. Zhu*. AI-based discovery of innovative therapeutic target. Invited speaker of domestic conference for The 15th National Symposium of Computer & Computational Chemistry. Fudan University, Shanghai, P. R. China (2019).

F. Zhu*. Machine learning-based discovery of innovative therapeutic target. Invited speaker of domestic conference for The 4th China Analytical Pharmacology Conference. Shenyang Pharmaceutical University, Shenyang, P. R. China (2019).

F. Zhu*. AI-based discovery of drug target for HIV infection. Invited speaker of domestic conference for Computational Drug Discovery and ACM Chinese Council. Central South University, Changsha, P. R. China (2019).

F. Zhu*. Therapeutic target discovery based on artificial intelligence. Invited speaker of international conference for 2019 Chinese Medicinal Chemistry Symposium & CPA-EFMC International Symposium on Medicinal Chemistry. Sichuan University, Chengdu, P. R. China (2019).

F. Zhu*. Simultaneous improvement in the precision, accuracy and robustness of label-free proteome quantification by optimizing data manipulation chains. Invited speaker of international conference for The Taizhou International Conference on Artificial Intelligence and Biomedical Research. Taizhou University, Taizhou, P. R. China (2019).

F. Zhu*. ANPELA: analysis and performance-assessment of the label-free quantification workflow for metaproteomic studies. Invited speaker of domestic conference for The 2019 Jiangsu-Zhejiang International Symposium of Bioinformatics and Computational Sciences. Jiangnan University, Wuxi, P. R. China (2019).

F. Zhu*. Consistent gene signature of schizophrenia identified by a novel feature selection strategy from comprehensive sets of transcriptomic data. Invited speaker of domestic conference for The 3rd Conference of Analytical Pharmacology. Zunyi Medical University, Zuiyi, P. R. China (2018).

F. Zhu*. Progression of first-in-class drugs and their corresponding targets. Invited speaker of domestic conference for The 10th National Symposium of Genetics Society of China. Nanjing Agricultural University, Nanjing, P. R. China (2018).

F. Zhu*. Proteomics-directed novel target discovery. Invited speaker of domestic conference for The 2018 Annual Symposium of the Shanghai Association of Chinese Integrative Medicine. Shanghai University of Traditional Chinese Medicine, Shanghai, P. R. China (2018).

F. Zhu*. Progression-speed differentiating features of the targets of first-in-class drugs. Invited speaker of domestic conference for The 14th Symposium of the Chinese Pharmaceutical Association for Youth Pharmacologist. Chinese Pharmaceutical Association, Hangzhou, P. R. China (2018).

F. Zhu*. Target discovery using proteomic and system biological data. Invited speaker of international conference for The 2nd Worldwide Chinese Computational Biology and Molecular Simulation Conference. Sun Yat-sen University, Guangzhou, P. R. China (2018).

F. Zhu*. OMICs based innovative drug target discovery. Invited speaker of domestic conference for The 31st Academic Annual Conference of the Chinese Chemical Society. Zhejiang University, Hangzhou, P. R. China (2018).

F. Zhu*. Next generation innovative therapeutic target from NOREVA. Invited speaker of international conference for Asian Federation for Pharmaceutical Sciences Conference 2017. Xiamen University, Xiamen, P. R. China (2017).

F. Zhu*. Target identification assisted by big-data analyzing tools. Invited speaker of domestic conference for The 14th National Symposium of Computer & Computational Chemistry. Nanjing University, Nanjing, P. R. China (2017).

F. Zhu*. Drug design and big-data platform. Invited speaker of domestic conference for The 5th Academic Forum for Postgraduates. Sichuan University, Chengdu, P. R. China (2017).

W. W. Xue*, F. Zhu*. What contributes to SNRIs’ dual-targeting mechanism? The key role played by TM6 domain. Invited speaker of domestic conference for The Second Conference on Innovative Drug Research and Application. Nanjing Biotech and Pharmaceutical Valley, Nanjing, P. R. China (2017).

F. Zhu*. Normalization and evaluation of metabolomics and proteomics data from multiple perspectives. Invited speaker of domestic conference for Bioinformatics and Intelligent Information Processing Academic Conference 2017 (BIIP2017). Shanghai Jiao Tong University, Shanghai, P. R. China (2017).

F. Zhu*. NOREVA: normalization and evaluation of MS-based metabolomics data. Invited speaker of domestic conference for The Fifth Young Scholars Forum for Interdisciplinary Researches in Mathematics, Computer Sciences and Biological Sciences. Academy of Mathematics and System Science, Chinese Academy of Sciences, Beijing, P. R. China (2017).

F. Zhu*. Normalization and evaluation of MS-based metabolomics data from multiple perspectives. Invited speaker of domestic conference for The 2017 (the second) Conference on Precision and Future Medicine. Zhejiang University, Hangzhou, P. R. China (2017).

F. Zhu*. Large-scale metabolomics data analysis. Invited speaker of domestic conference for China Society of Biotechnology Young Scientists Forum II. South China University of Technology, Guangzhou, P. R. China (2017).

F. Zhu*. Bioinformatics strategies in precision medicine. Invited speaker of international conference for The 2016 Symposium of Guanghua Young Distinguished Scholars. Fudan University, Shanghai, P. R. China (2016).

F. Zhu*. Insight into the pathogenesis of pituitary adenomas by analyzing trans-omic data. Invited speaker of international conference for BIT’s 6th Annual International Congress of Medichem-2016 (ICM-2016). China Pharmaceutical University, Nanjing, P. R. China (2016).

F. Zhu*. Metabolomics meta-analysis by MMEASE. Invited speaker of international conference for The 1st International Symposium on Targeted Therapeutics and Molecular Medicine (ISTTMM 2016). Chongqing University of Arts and Sciences, Chongqing, P. R. China (2016).

W. W. Xue, F. Zhu*. Molecular dynamics study and comparison on the binding modes of SSRIs, sNRIs and SNRIs antidepressants. Invited speaker of international conference for BIT’s 6th Annual International Congress of Medichem-2016 (ICM-2016). China Pharmaceutical University, Nanjing, P. R. China (2016).

G. X. Zheng, W. W. Xue, F. Zhu*. Exploring the inhibitory mechanism of approved selective norepinephrine reuptake inhibitors from molecular dynamics study. Invited speaker of international conference for The 4th International Conference on Molecular Simulation (ICMS 2016). Shanghai Jiao Tong University, Shanghai, P. R. China (2016).

F. Zhu*. Normalization and meta-analysis of metabolomics data. Invited speaker of domestic conference for The 7th National Conference on Bioinformatics & System Biology. University of Electronic Science and Technology of China, Chengdu, P. R. China (2016).

F. Zhu*. Insight into the pathogenesis of pituitary adenomas by meta-analysis of transcriptomic and metabolomic Data. Invited speaker of domestic conference for The 2016 Conference on Precision Medicine. Xian Jiaotong University, Xian, P. R. China (2016).

F. Zhu*. Identification of the inhibitory mechanism of FDA approved selective serotonin reuptake inhibitors: an insight from molecular dynamics simulation study. Invited speaker of international conference for The 12th Sino-US Chemistry Professors Conference. Sun Yat-sen University, Guangzhou, P. R. China (2016).

F. Zhu*. Discovering the stable marker identification methods for metabonomics study. Invited speaker of international conference for The 2016 Symposium of International Young Distinguished Scholars. Tongji University, Shanghai, P. R. China (2016).

F. Zhu*. Design of multi-target anticancer drugs by analyzing the protein-protein interaction network of cancer. Invited speaker of domestic conference for The 2nd Symposium on Bioinformatics and Drug Design. Chongqing University, Chongqing, P. R. China (2016).

F. Zhu*. Meta-analysis of metabolomic data. Invited speaker of domestic conference for The 2016 Conference on Bioinformatics and Intelligent Information Processing (BIIP2016). Jilin University, Jilin, P. R. China (2016).

F. Zhu*. MMEASE: a web-server for meta-analysis of metabolomic data by enhanced metabolite annotation, marker selection and enrichment analysis. Invited speaker of domestic conference for The 30th Academic Annual Conference of the Chinese Chemical Society. Dalian University of Technology, Dalian, P. R. China (2016).

F. Zhu*. Identifying the metabonomics biomarkers. Invited speaker of domestic conference for The 2016 Academic Salon of Shanghai Society for Bioinformatics. Fudan University, Shanghai, P. R. China (2016).

F. Zhu*. Insight into the pathogenesis of pituitary adenomas by meta-analysis of transcriptomic data. Invited speaker of domestic conference for The 2016 Symposium of Big Data and Precision Biomedical Informatics. Shanghai Jiao Tong University, Shanghai, P. R. China (2016).

W. W. Xue and F. Zhu*. Identification of multi-target drug against remote target pair using combinatorial support vector mechine method. Invited speaker of domestic conference for The 13th National Symposium of Computer & Computational Chemistry. Sun Yat-sen University, Guangzhou, P. R. China (2015).

F. Zhu*. Future bioprospecting: from the clustered patterns of species origins of nature-derived drugs. Invited speaker of international conference for The 6th International Conference of Molecular Simulation and Applied Information Technologies (6th-ICMS&I). China Pharmaceutical University, Nanjing, P. R. China (2012).

F. Zhu*. Drug discovery prospect from untapped species: indications from approved natural product drugs. Invited speaker of international conference for International Symposium on Natural Product Synthesis and Innovative Process Methods for Drug Manufacture. Chongqing University, Chongqing, P. R. China (2012).

F. Zhu*. Identification of next generation innovative therapeutic targets: clues from genetic, structural, physicochemical and system profile of successful ones. Invited speaker of international conference for Singapore Symposium on Computational Biology 2009 (SYMBIO2009). National University of Singapore, Singapore, Singapore (2009).

Invited Academic Visit and Presentation (click to show or hide the details)

F. Zhu*. Bioinformatics tools applied to the research field of brain science. Invited academic visit by Prof. Bo-Chu Wang to Bioengineering College, Chongqing University, Chongqing, P. R. China (2016).

F. Zhu*. Comprehensive assessment of the popular normalization methods used in metabonomics study. Invited academic visit by Prof. Yu-Yang Jiang to Graduate School at Shenzhen, Tsinghua University, Shenzhen, P. R. China (2016).

W. W. Xue and F. Zhu*. Extension of bioinformatics to the fields of brain sciences: metabonomics study of pituitary adenomas and design of multi-target antidepressants. Invited academic visit by Prof. Han-Bing Rao to Faculty of Science, Sichuan Agricultural University, Yaan, P. R. China (2016).

W. W. Xue and F. Zhu*. Design of multi-target anticancer drugs by analyzing the protein-protein interaction network of cancer. Invited academic visit by Prof. Xiao-Jun Yao to School of Pharmacy, Lanzhou University, Lanzhou, P. R. China (2014).

F. Zhu*. Computer-aided drug design based on the complex biological network of cancer. Invited academic visit by Prof. Cheng-Zhi Huang to College of Pharmaceutical Sciences and Chinese Medicine, Southwest University, Chongqing, P. R. China (2014).

F. Zhu*. Identification of multi-target anticancer leads using combinatorial machine learning methods. Invited academic visit by Prof. Wei Wang to State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou, P. R. China (2013).

F. Zhu*. Design of anticancer leads and testing of their bioactivities. Invited academic visit by Prof. Da-He Liu to Department of Physics, Beijing Normal University, Beijing, P. R. China (2013).

F. Zhu*. Find target and design bullet for the complex network disease - cancer. Invited academic visit by Prof. Ying Xue to College of Chemistry, Sichuan University, Chengdu, P. R. China (2013).

F. Zhu*. Targets! Bullets! Computer-aided drug design from the network medicine perspective. Invited academic visit by Prof. Han-Bing Rao to Faculty of Science, Sichuan Agricultural University, Yaan, P. R. China (2013).

F. Zhu*. Bioinformatics identification of anticancer drug targets. Invited academic visit by Prof. Kun-Xian Shu to School of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, P. R. China (2013).

F. Zhu*. Clustered patterns of species origins of active ingredients in the traditional chinese medicine. Invited academic visit by Prof. Qi-Ni Qian to Chongqing Institute of Medicinal Plant Cultivation, Chongqing Institute of Medicinal Plant Cultivation, Chongqing, P. R. China (2013).

IDRB: Innovative Drug Research and Bioinformatics Group

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