,
-

AIDD8121, Research Methodology and Ethics

AIDD8299, Thesis

Biography: Dr. Jingjing Guo obtained her Ph.D. degree in medicinal chemistry from Lanzhou University in 2015. She joined the Center for Artificial Intelligence Driven Drug Discovery (AIDD) at Macao Polytechnic University in 2022. She has made a series of innovative achievements in computational biology and drug discovery. Now she has published more than 80 SCI papers, including Chemical Reviews, Elife, Angewandte Chemie International Edition, WIREs Computational Molecular Science, and other international authoritative journals. She has served as Associate Editor of Current Research in Structural Biology since January 2024.  

ORCID | Scopus | Google Scholar | ResearchGate

AI4S——让智能重塑生命科学未来！

  • 通过“干湿结合、闭环迭代”的智能研发模式，研究成果将应用于创新药物开发、绿色生物制造与精准医疗等领域，让智能重塑生命科学未来！
  • 目前课题组开放多个硕博士名额，欢迎对AI酶设计、AI抗体设计、AI功能蛋白设计、智能药物发现、生物信息学、医学AI等方向感兴趣的同学加入！

  • Current Employer/Organization

    Macao Polytechnic University

  • Current Position

    Professor

    Macao Polytechnic University

  • Subjects Taught

    AIDD8121, Research Methodology and Ethics

    AIDD8299, Thesis

  • Education

    2009-2015: Ph.D. in Medicinal Chemistry, Lanzhou University, China
    2013-2015: Visiting Ph.D. student in Biophysics, Florida State University, United States
    2005-2009: B.S. in Chemistry, Hebei Normal University, China

  • Research Interests

    Ø  Artificial intelligence and functional protein design 

    Ø  Rational design of enzymes

    Ø  Artificial intelligence and drug discovery

  • Work Experience

    2022-present: Professor, Macao Polytechnic University
    2019-2022: Professor, Nanjing Agricultural University, China
    2017-2019: Research Fellow, Nanyang Technological University, Singapore

  • Publications

    Selected publications:

    • Fan D, Li M, Shen Z, Li Y, Guo J*, Wang D*, Han T*, Tang B Z.* Boosting the Antimicrobial Activity of Quaternary Ammonium Photosensitizers by Janus‐Type AIE Luminogens. Aggregate, 2025. http://dx.doi.org/10.1002/agt2.70087
    • Sui, J.; Cui, W.; Zhang, X.; Duan, H.; Guo, J.* Human miRNA-disease Association Prediction Via Residual GraphSAGE With Nonlinear Adaptive Feature Fusion and Triplet Contrastive Learning. J. Mol. Biol. 2025, 437, 169360.

      http://dx.doi.org/10.1016/j.jmb.2025.169360

    • Li, X. K.; Tang, L. J.; Li, Z. Y.; Qiu, D.; Yang, Z. L.; Zhang, X. Y.; Zhang, X. Z.; Guo, J.*; Li, B.* Geographical origin discrimination of Chenpi using machine learning and enhanced mid-level data fusion. npj Sci. Food 2025, 9, 17.

      http://dx.doi.org/10.1038/s41538-025-00376-0

    • He, B.; Mao, L.; Xi, L.; Guo, J.* Synergistic insights into positive allosteric modulator and agonist using Gaussian accelerated and tau random acceleration simulations in the metabotropic glutamate receptor 2. Neuropharmacology 2025, 269, 110351.

      http://dx.doi.org/10.1016/j.neuropharm.2025.110351

    • Ye, Y.; Jiang, H.; Xu, R.; Wang, S.; Zheng, L.*; Guo, J.* The INSIGHT platform: Enhancing NAD(P)-dependent specificity prediction for co-factor specificity engineering. International Journal of Biological Macromolecules 2024, 135064. http://dx.doi.org/10.1016/j.ijbiomac.2024.135064
    • Xu, R.; Pan, Q.; Zhu, G.; Ye, Y.; Xin, M.; Wang, Z.; Wang, S.; Li, W.; Wei, Y.; Guo, J.*; Zheng, L.* ThermoLink: Bridging disulfide bonds and enzyme thermostability through database construction and machine learning prediction. Protein Science 2024, 33, e5097. http://dx.doi.org/10.1002/pro.5097
    • Li, X.; Zhang, F.; Zheng, L.*; Guo, J.* Advancing ecotoxicity assessment: Leveraging pre-trained model for bee toxicity and compound degradability prediction. J. Hazard. Mater. 2024, 475, 134828.

      http://dx.doi.org/10.1016/j.jhazmat.2024.134828

    • Luo, Q.; Wang, S.; Li, H. Y.; Zheng, L.*; Mu, Y.*; Guo, J.* Benchmarking reverse docking through AlphaFold2 human proteome. Protein Sci. 2024, 33, e5167.

      http://dx.doi.org/10.1002/pro.5167

    • Yuan, L.; Guo, J.* PharmaRedefine: A database server for repurposing drugs against pathogenic bacteria. METHODS 2024, 227, 78-85. http://dx.doi.org/10.1016/j.ymeth.2024.05.011

    • Shi, L.; Zhao, W.; Jiu, Z.; Guo, J.*; Zhu, Q.; Sun, Y.; Zhu, B.; Chang, J.; Xin, P.* Redox-Regulated Synthetic Channels: Enabling Reversible Ion Transport by Modulating the Ion-Permeation Pathway. Angew Chem Int Ed Engl 2024, e202403667. http://dx.doi.org/10.1002/anie.202403667

    • Bao, Y.; Jia, F.; Li, M.; Xu, R.; Xie, Y.; Zhang, F.*; Guo, J.* Characterizing the Molecular Mechanism of the Lethal C423D Mutation in FgMyoI: A Molecular Perspective. J Agric Food Chem 2024, 72, 1539-1549. http://dx.doi.org/10.1021/acs.jafc.3c08648

    • Guo, J.*; Bao, Y. Q.; Li, M. R.; Li, S.; Xi, L. L.; Xin, P. Y.; Wu, L.; Liu, H. X.; Mu, Y. G. Application of computational approaches in biomembranes: From structure to function. Wiley Interdisciplinary Reviews-Computational Molecular Science 2023, 13, e1679. http://dx.doi.org/10.1002/wcms.1679

    • Xin, P.*; Xu, L.; Dong, W.; Mao, L.; Guo, J.*; Bi, J.; Zhang, S.; Pei, Y.; Chen, C. P.*, Synthetic K(+) Channels Constructed by Rebuilding the Core Modules of Natural K(+) Channels in an Artificial System. Angew. Chem. Int. Ed. Engl., 2023, 62, e202217859.
    • J. Guo; H. X. Zhou, Allosteric activation of SENP1 by SUMO1 beta-grasp domain involves a dock-and-coalesce mechanism. Elife, 2016, 5, e18249.
    • J. Guo; H.X. Zhou, Protein allostery and conformational dynamics. Chem. Rev., 2016, 116, 6503.

  • Description

    Research Interests:

    • AI-driven protein design and modification
    • AI-empowered drug repositioning and drug discovery
    • Artificial intelligence and healthcare big data 


    Tools and Resources:

    • EcoToxPred [1]: capable of predicting ecotoxicity, specifically the toxicity of molecules to bees and the ecological degradation potential of molecules.
    • INSIGHT [2]: an expansive dataset and predictive model for NAD(P)H coenzyme specificity.
    • ThermoLink [3]: a comprehensive dataset containing the effect of disulfide bonds on the protein thermostability.
    • PharmaRedefine [4]: a database server for repurposing drugs against pathogenic bacteria.
    • AutoRevDock [5]: an open-source toolkit for scalable reverse docking.


    1. Li X, Zhang F, Zheng L, Guo J. Advancing ecotoxicity assessment: Leveraging pre-trained model for bee toxicity and compound degradability prediction. J. Hazard. Mater., 2024, 475, 134828
    2. Ye Y, Jiang H, Xu R, Wang S, Zheng L, Guo J. The INSIGHT platform: Enhancing NAD(P)-dependent specificity prediction for co-factor specificity engineering. Int. J. Biol. Macromol., 2024, 278, 135064
    3. Xu R, Pan Q, Zhu G, Ye Y, Xin M, Wang Z, Wang S, Li W, Wei Y, Guo J, Zheng L. ThermoLink: Bridging disulfide bonds and enzyme thermostability through database construction and machine learning prediction. Protein Sci., 2024, 33, e5097
    4. Yuan L, Guo J. PharmaRedefine: A database server for repurposing drugs against pathogenic bacteria. Methods, 2024, 227, 78
    5. Luo Q, Guo J. et al. AutoRevDock: An Open-Source Toolkit for Scalable Reverse Docking. Under Review.

  • Journal papers

    2025

    • Fan D, Li M, Shen Z, Li Y, Guo J*, Wang D*, Han T*, Tang B Z*. Boosting the Antimicrobial Activity of Quaternary Ammonium Photosensitizers by Janus‐Type AIE Luminogens. Aggregate, 2025. http://dx.doi.org/10.1002/agt2.70087
    • Cui W, Ye Y, Guo J*, Yao X*, Tong H H Y*. Comparative multi-task deep learning models for protein-nucleic acid interaction prediction: Unveiling the superior efficacy of the PNI-MAMBA architecture. Int. J. Biol. Macromol., 2025, 147419. http://dx.doi.org/10.1016/j.ijbiomac.2025.147419
    • Gao M, Cui W, Duan H, Guo J*. DNA methylation subtypes dictate metastatic heterogeneity of osteosarcoma via distinct tumor-stromal interactions: Multi-omics profiling and decitabine validation. Int. J. Biol. Macromol., 2025, 147473. http://dx.doi.org/10.1016/j.ijbiomac.2025.147473
    • Sui J, Cui W, Zhang X, Duan H, Guo J*. Human miRNA-disease Association Prediction Via Residual GraphSAGE With Nonlinear Adaptive Feature Fusion and Triplet Contrastive Learning. J. Mol. Biol., 2025, 437, 169360. http://dx.doi.org/10.1016/j.jmb.2025.169360
    • Li L, Luo Q, Yang S, Wang H, Mu Y, Guo J, Zhang F. Unraveling the molecular mechanism of FgGcn5 inhibition by phenazine-1-carboxamide: combined in silico and in vitro studies. Pest Manag Sci, 2025, 81, 937. http://dx.doi.org/10.1002/ps.8496
    • Bao Y, Jia F, Geng Y, Song G, Xu R, Wang H, Mu Y, Tong H H Y, Zhang F, Guo J. Uncovering the Differed Susceptibility of Fusarium oxysporum (Fo32931 and FocII5) to Fungicide Phenamacril: From Computational and Experimental Perspectives. J. Agric. Food. Chem., 2025, 73, 189. http://dx.doi.org/10.1021/acs.jafc.4c07865
    • Li X K, Tang L J, Li Z Y, Qiu D, Yang Z L, Zhang X Y, Zhang X Z, Guo J J, Li B Q. Geographical origin discrimination of Chenpi using machine learning and enhanced mid-level data fusion. npj Sci. Food, 2025, 9, 17. http://dx.doi.org/10.1038/s41538-025-00376-0
    • Jiao F, Xu R, Luo Q, Li X, Tong H H Y, Guo J. Elucidating allosteric signal disruption in PBP2a: impact of N146K/E150K mutations on ceftaroline resistance in methicillin-resistant Staphylococcus aureus. J. Comput.-Aided Mol. Des., 2025, 39. http://dx.doi.org/10.1007/s10822-025-00584-6
    • He B, Mao L, Xi L, Guo J. Synergistic insights into positive allosteric modulator and agonist using Gaussian accelerated and tau random acceleration simulations in the metabotropic glutamate receptor 2. Neuropharmacology, 2025, 269, 110351. http://dx.doi.org/10.1016/j.neuropharm.2025.110351
    • Jiao F, Wang P, Zeng D, Bao Y, Zhang Y, Tao J, Guo J. Identification of Potential PBP2a Inhibitors Against Methicillin-Resistant Staphylococcus aureus via Drug Repurposing and Combination Therapy. Chem. Biol. Drug Des., 2025, 105, e70088. http://dx.doi.org/10.1111/cbdd.70088
    • He B, Mao L, Jin X, Duan H, Guo J. Unveiling the molecular mechanism of G(i) protein biased activation at mGlu(2)-mGlu(4) heterodimers through Gaussian accelerated molecular dynamics simulations. Protein Sci., 2025, 34, e70277. http://dx.doi.org/10.1002/pro.70277
    • Sui J, Cui W, Zhang X, Duan H, Guo J. Human miRNA-disease Association Prediction Via Residual GraphSAGE With Nonlinear Adaptive Feature Fusion and Triplet Contrastive Learning. J. Mol. Biol., 2025, 437, 169360. http://dx.doi.org/10.1016/j.jmb.2025.169360
    • Zeng D, Jiao F, Yang Y, Dou S, Yu J, Yu X, Zhou Y, Xue J, Li X, Duan H, Zhang Y, Guo J, Yang W. Myricetin Potentiates Antibiotics Against Resistant Pseudomonas aeruginosa by Disrupting Biofilm Formation and Inhibiting Motility Through FimX-Mediated c-di-GMP Signaling Interference. Biology (Basel), 2025, 14. http://dx.doi.org/10.3390/biology14070859
    • Zhang J, Jiao F, Ge Y, Cheng B, Guo J. Antibiotic Susceptibility Evaluation in Bacterial Infections from Orthopedic Inpatients with Leg Trauma. Curr. Microbiol., 2025, 82, 476. http://dx.doi.org/10.1007/s00284-025-04458-w


    2024

    • Zhang Y, Jiao F, Zeng D, Yu X, Zhou Y, Xue J, Yang W, Guo J. Synergistic Effects of Pyrrosia lingua Caffeoylquinic Acid Compounds with Levofloxacin Against Uropathogenic Escherichia coli: Insights from Molecular Dynamics Simulations, Antibiofilm, and Antimicrobial Assessments. Molecules, 2024,29, 5679. http://dx.doi.org/10.3390/molecules29235679
    • Yuan L, Guo J. PharmaRedefine: A database server for repurposing drugs against pathogenic bacteria. Methods, 2024, 227, 78. http://dx.doi.org/10.1016/j.ymeth.2024.05.011
    • Ye Y, Jiang H, Xu R, Wang S, Zheng L, Guo J. The INSIGHT platform: Enhancing NAD(P)-dependent specificity prediction for co-factor specificity engineering. Int. J. Biol. Macromol., 2024, 278, 135064. http://dx.doi.org/10.1016/j.ijbiomac.2024.135064
    • Xu R, Pan Q, Zhu G, Ye Y, Xin M, Wang Z, Wang S, Li W, Wei Y, Guo J, Zheng L. ThermoLink: Bridging disulfide bonds and enzyme thermostability through database construction and machine learning prediction. Protein Sci., 2024, 33, e5097. http://dx.doi.org/10.1002/pro.5097
    • Xu R, Bao Y, Jiao F, Li M, Zhang X, Zhang F, Guo J. Unraveling the atomic mechanisms underlying glyphosate insensitivity in EPSPS: implications of distal mutations. J. Biomol. Struct. Dyn., 2024, 1. http://dx.doi.org/10.1080/07391102.2024.2318472
    • Shi L, Zhao W, Jiu Z, Guo J, Zhu Q, Sun Y, Zhu B, Chang J, Xin P. Redox-Regulated Synthetic Channels: Enabling Reversible Ion Transport by Modulating the Ion-Permeation Pathway. Angew Chem Int Ed Engl, 2024, 63, e202403667. http://dx.doi.org/10.1002/anie.202403667
    • Mao L, Hou S, Shi L, Guo J, Zhu B, Sun Y, Chang J, Xin P. Synthetic anion channels: achieving precise mimicry of the ion permeation pathway of CFTR in an artificial system. Chem. Sci., 2024. http://dx.doi.org/10.1039/d4sc06893a
    • Luo Q, Wang S, Li H Y, Zheng L, Mu Y, Guo J. Benchmarking reverse docking through AlphaFold2 human proteome. Protein Sci., 2024, 33, e5167. http://dx.doi.org/10.1002/pro.5167
    • Li X, Zhang F, Zheng L, Guo J. Advancing ecotoxicity assessment: Leveraging pre-trained model for bee toxicity and compound degradability prediction. J. Hazard. Mater., 2024, 475, 134828. http://dx.doi.org/10.1016/j.jhazmat.2024.134828
    • Li M, Zhang X, Li S, Guo J. Unraveling the Interplay of Extracellular Domain Conformational Changes and Parathyroid Hormone Type 1 Receptor Activation in Class B1 G Protein-Coupled Receptors: Integrating Enhanced Sampling Molecular Dynamics Simulations and Markov State Models. ACS Chem. Neurosci., 2024, 15, 844. http://dx.doi.org/10.1021/acschemneuro.3c00747
    • Jiao F, Cui W, Wang P, Tong H H Y, Guo J, Tao J. Synergistic inhibition mechanism of quinazolinone and piperacillin on penicillin-binding protein 2a: a promising approach for combating methicillin-resistant Staphylococcus aureus. J. Biomol. Struct. Dyn., 2024, 1. http://dx.doi.org/10.1080/07391102.2024.2330708
    • Guo J, Liu H. The Applications of Molecular Dynamics Simulation in Studying Protein Structure and Dynamics. Curr. Med. Chem., 2024, 31, 2839. http://dx.doi.org/http://dx.doi.org/10.2174/092986733120240405144035
    • Bao Y, Xu R, Guo J. The multiple-action allosteric inhibition of TYK2 by deucravacitinib: Insights from computational simulations. Comput. Biol. Chem., 2024, 113, 108224. http://dx.doi.org/10.1016/j.compbiolchem.2024.108224
    • Bao Y, Jia F, Lin Y, Song G, Li M, Xu R, Wang H, Zhang F, Guo J. Unveiling the Mechanism of Phenamacril Resistance in F. graminearum: Computational and Experimental Insights into the C423A Mutation in FgMyoI. J. Agric. Food. Chem., 2024, 72, 15653. http://dx.doi.org/10.1021/acs.jafc.4c03467
    • Bao Y, Jia F, Li M, Xu R, Xie Y, Zhang F, Guo J. Characterizing the Molecular Mechanism of the Lethal C423D Mutation in FgMyoI: A Molecular Perspective. J. Agric. Food. Chem., 2024, 72, 1539. http://dx.doi.org/10.1021/acs.jafc.3c08648


    2022-2023

    • Xu R, Bao Y, Li M, Zhang Y, Xi L, Guo J. Computational Insights into the Allosteric Modulation of a Phthalate-Degrading Hydrolase by Distal Mutations. Biomolecules, 2023,13, 443. http://dx.doi.org/10.3390/biom13030443
    • Xin P, Xu L, Dong W, Mao L, Guo J, Bi J, Zhang S, Pei Y, Chen C P. Synthetic K(+) Channels Constructed by Rebuilding the Core Modules of Natural K(+) Channels in an Artificial System. Angew Chem Int Ed Engl, 2023, 62, e202217859. http://dx.doi.org/10.1002/anie.202217859
    • Xi L, Shi A, Shen T, Wang G, Wei Y, Guo J. Licraside as novel potent FXR agonist for relieving cholestasis: structure-based drug discovery and biological evaluation studies. Front. Pharmacol., 2023, 14, 1197856. http://dx.doi.org/10.3389/fphar.2023.1197856
    • Li M, Bao Y, Xu R, Li M, Xi L, Guo J. Understanding the Allosteric Modulation of PTH1R by a Negative Allosteric Modulator. Cells, 2023, 12, 41. http://dx.doi.org/10.3390/cells12010041
    • Li M, Bao Y, Li M, Guo J. GPCR Allostery: A View from Computational Biology. Curr. Med. Chem., 2023, 30, 4533. http://dx.doi.org/10.2174/0929867330666230113125246
    • Jiao F, Bao Y, Li M, Zhang Y, Zhang F, Wang P, Tao J, Tong H H Y, Guo J. Unraveling the mechanism of ceftaroline-induced allosteric regulation in penicillin-binding protein 2a: insights for novel antibiotic development against methicillin-resistant Staphylococcus aureus. Antimicrob. Agents Chemother., 2023, 67, e0089523. http://dx.doi.org/10.1128/aac.00895-23
    • Guo J J, Bao Y Q, Li M R, Li S, Xi L L, Xin P Y, Wu L, Liu H X, Mu Y G. Application of computational approaches in biomembranes: From structure to function. Wiley Interdisciplinary Reviews-Computational Molecular Science, 2023, 13, e1679. http://dx.doi.org/10.1002/wcms.1679
    • Bao Y, Xu Y, Jia F, Li M, Xu R, Zhang F, Guo J. Allosteric inhibition of myosin by phenamacril: a synergistic mechanism revealed by computational and experimental approaches. Pest Manag Sci, 2023, 79, 4977. http://dx.doi.org/10.1002/ps.7699
    • Li M, Li M, Xie Y, Guo J. Uncovering the Molecular Basis for the Better Gefitinib Sensitivity of EGFR with Complex Mutations over Single Rare Mutation: Insights from Molecular Simulations. Molecules, 2022, 27, 3844. http://dx.doi.org/10.3390/molecules27123844
    • Li M, Bao Y, Xu R, Zhang X, La H, Guo J. Mechanism of enhanced sensitivity of mutated beta-adrenergic-like octopamine receptor to amitraz in honeybee Apis mellifera: An insight from MD simulations. Pest Manag Sci, 2022, 78, 5423. http://dx.doi.org/10.1002/ps.7164
    • Li M, Bao Y, Xu R, La H, Guo J. Critical Extracellular Ca2+ Dependence of the Binding between PTH1R and a G-Protein Peptide Revealed by MD Simulations. ACS Chem. Neurosci., 2022, 13, 1666. http://dx.doi.org/10.1021/acschemneuro.2c00176
    • Bao Y, Li M, Xie Y, Guo J. Investigating the Permeation Mechanism of Typical Phthalic Acid Esters (PAEs) and Membrane Response Using Molecular Dynamics Simulations. Membranes, 2022, 12, 596. http://dx.doi.org/10.3390/membranes12060596
    • Li M, Xu Y, Guo J. Insights into the negative regulation of EGFR upon the binding of an allosteric inhibitor. Chem. Biol. Drug Des., 2022, 99, 650. http://dx.doi.org/10.1111/cbdd.14033
    • Li M, Li M, Guo J. Molecular Mechanism of Ca(2+) in the Allosteric Regulation of Human Parathyroid Hormone Receptor-1. J. Chem. Inf. Model., 2022, 62, 5110. http://dx.doi.org/10.1021/acs.jcim.1c00471

聚焦AI驱动的酶与蛋白质设计，引领智能蛋白大分子发现新范式


郭晶晶课题组隶属于澳门理工大学应用科学学院人工智能药物发现中心（CAIDD），致力于推动“IT+BT”（信息技术 + 生物技术）的深度交叉融合。课题组以人工智能蛋白质设计为核心研究方向，专注于AI赋能的酶工程与蛋白质从头设计，利用前沿深度学习、生成式AI、多模态大数据分析等技术，开展功能性酶的智能创制、高活性/高稳定性蛋白的逆向设计、以及治疗性蛋白的智能化开发。

我们聚焦以下研究方向：
- 基于生成式AI的蛋白质结构与功能预测
- 从头蛋白设计（de novo protein design）与酶活性中心智能重构
- 利用大模型进行定向进化模拟与突变效应预测
-  AI驱动的生物药设计与优化（如抗体、多肽、融合蛋白等）
- 融合生物信息学与机器学习的高通量数据挖掘与智能实验闭环


通过“干湿结合、闭环迭代”的智能研发模式，研究成果将应用于创新药物开发、绿色生物制造与精准医疗等领域，让智能重塑生命科学未来！


目前课题组开放多个硕博士名额，欢迎对AI酶设计、AI抗体设计、AI功能蛋白设计、智能药物发现、生物信息学、医学AI等方向感兴趣的同学踊跃申请！

2026 Fall Ph.D. students recruiting

Our research group was established in 2022 and is affiliated with the Artificial Intelligence Drug Discovery Center at Macau Polytechnic University. With a focus on "IT+BT," our research primarily revolves around AI-based protein and drug design, integrating information technology and biotechnology to advance life science research through molecular modeling, artificial intelligence, and big data technologies.

Professor Guo Jingjing's research group welcomes students or scholars who are passionate about research and possess a team spirit to join us. We welcome students interested in protein engineering and design, computer-aided drug design, artificial intelligence-driven drug design, bioinformatics, and related fields to join our research team and contribute to the deep integration of "IT" and "BT."

There are several positions available for master's and Ph.D. students. We welcome applications!

Interested individuals are requested to send their resumes and contact information to: jguo@mpu.edu.mo.