Academic Outputs (2024)
人工智能藥物發現中心學術成果年度報告 2024 (*top journal)
Academic outputs from Centre of Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, MPU (2024) [*top journal]
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Zhai X, Tong HHY, Lam CK, Xing A, Sha Y, Luo G, Meng W, Li J, Zhou M, Huang Y, et al: Association and causal mediation between marital status and depression in seven countries. Nature Human Behaviour 2024. (JCR: Q1; IF: 21.4) *
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Wang L, Zhang Q, Tong HHY, Yao X, Liu H, Li G: Computational methods for unlocking the secrets of potassium channels: Structure, mechanism, and drug design. Wiley Interdisciplinary Reviews: Computational Molecular Science 2024, 14. (JCR: Q1; IF: 16.8) *
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Li S, Peng L, Chen L, Que L, Kang W, Hu X, Ma J, Di Z, Liu Y: Discovery of Highly Bioactive Peptides through Hierarchical Structural Information and Molecular Dynamics Simulations. Journal of Chemical Information and Modeling 2024, 64:8164-8175. (JCR: Q1; IF: 5.6) *
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Li X, Zhang F, Zheng L, Guo J: Advancing ecotoxicity assessment: Leveraging pre-trained model for bee toxicity and compound degradability prediction. Journal of Hazardous Materials 2024, 475. (JCR: Q1; IF: 12.2) *
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Gu S, Yang Y, Zhao Y, Qiu J, Wang X, Tong HHY, Liu L, Wan X, Liu H, Hou T, Kang Y: Evaluation of AlphaFold2 Structures for Hit Identification across Multiple Scenarios. Journal of Chemical Information and Modeling 2024, 64:3630-3639. (JCR: Q1; IF: 5.6) *
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Wang L, Li S, Xiang S, Liu H, Sun H: Elucidating the Selective Mechanism of Drugs Targeting Cyclin-Dependent Kinases with Integrated MetaD-US Simulation. Journal of Chemical Information and Modeling 2024, 64:6899-6911. (JCR: Q1; IF: 5.6) *
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Gong X, Li S, Huang J, Tan S, Zhang Q, Tian Y, Li Q, Wang L, Tong HHY, Yao X, et al: Discovery of potent LRRK2 inhibitors by ensemble virtual screening strategy and bioactivity evaluation. European Journal of Medicinal Chemistry 2024, 279. (JCR: Q1; IF: 6) *
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Zhu Y, Mou X, Song Y, Zhang Q, Sun B, Liu H, Tang H, Bao R: Molecular mechanism of the one-component regulator RccR on bacterial metabolism and virulence. Nucleic Acids Research 2024, 52:3433-3449. (JCR: Q1; IF: 16.6) *
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Yue Y, Li S, Cheng Y, Wang L, Hou T, Zhu Z, He S: Integration of molecular coarse-grained model into geometric representation learning framework for protein-protein complex property prediction. Nature Communications 2024, 15. (JCR: Q1; IF: 14.7) *
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Wang X, Yin X, Jiang D, Zhao H, Wu Z, Zhang O, Wang J, Li Y, Deng Y, Liu H, et al: Multi-modal deep learning enables efficient and accurate annotation of enzymatic active sites. Nature Communications 2024, 15. (JCR: Q1; IF: 14.7) *
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Wang M, Li S, Wang J, Zhang O, Du H, Jiang D, Wu Z, Deng Y, Kang Y, Pan P, Li D, Wang X, Yao X, Hou T, Hsieh CY. ClickGen: Directed exploration of synthesizable chemical space via modular reactions and reinforcement learning. Nature Communications 2024, 15:10127. (JCR: Q1; IF: 14.7) *
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Dong Y, Ma T, Xu T, Feng Z, Li Y, Song L, Yao X, Ashby CR, Hao GF: Characteristic roadmap of linker governs the rational design of PROTACs. Acta Pharmaceutica Sinica B 2024, 14:4266-4295. (JCR: Q1; IF: 14.7) *
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Li P, Zhang K, Liu T, Lu R, Chen Y, Yao X, Gao L, Zeng X: A deep learning approach for rational ligand generation with toxicity control via reactive building blocks. Nature Computational Science 2024. (IF: 12) *
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Liu C, Wu L, Li G, Xiao W, Tan L, Xu D, Guo J: AI-based 3D pipe automation layout with enhanced ant colony optimization algorithm. Automation in Construction 2024, 167. (JCR: Q1; IF: 9.6) *
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Gu S, Bao L, Yang Y, Zhao Y, Tong HHY, Liu L, Liu H, Hou T, Kang Y: AMGC is a multiple-task graph neutral network for epigenetic target profiling. Cell Reports Physical Science 2024, 5. (JCR: Q1; IF: 7.9) *
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Li P, Jiang Z, Liu T, Liu X, Qiao H, Yao X: Improving drug response prediction via integrating gene relationships with deep learning. Briefings in Bioinformatics 2024, 25. (JCR: Q1; IF: 6.8) *
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Wang R, Wang T, Zhuo L, Wei J, Fu X, Zou Q, Yao X: Diff-AMP: tailored designed antimicrobial peptide framework with all-in-one generation, identification, prediction and optimization. Briefings in Bioinformatics 2024, 25. (JCR: Q1; IF: 6.8) *
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Zhu C, Zhang C, Shang T, Zhang C, Zhai S, Cao L, Xu Z, Su Z, Song Y, Su A, et al: GAPS: a geometric attention-based network for peptide binding site identification by the transfer learning approach. Briefings in Bioinformatics 2024, 25. (JCR: Q1; IF: 6.8) *
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Zhang C, Zhang C, Shang T, Zhu N, Wu X, Duan H: HighFold: accurately predicting structures of cyclic peptides and complexes with head-to-tail and disulfide bridge constraints. Briefings in Bioinformatics 2024, 25. (JCR: Q1; IF: 6.8) *
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Zhong H, Wang X, Chen S, Wang Z, Wang H, Xu L, Hou T, Yao X, Li D, Pan P: Discovery of Novel Inhibitors of BRD4 for Treating Prostate Cancer: A Comprehensive Case Study for Considering Water Networks in Virtual Screening and Drug Design. Journal of Medicinal Chemistry 2024, 67:138-151. (JCR: Q1; IF: 6.8) *
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Zhang J, Wang R, Wei L: MucLiPred: Multi-Level Contrastive Learning for Predicting Nucleic Acid Binding Residues of Proteins. Journal of Chemical Information and Modeling 2024, 64:1050-1065. (JCR: Q1; IF: 5.6) *
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Cheong HH, Zuo W, Chen J, Un CW, Si YW, Wong KH, Kwok HF, Siu SWI: Identification of Anticancer Peptides from the Genome of Candida albicans: in Silico Screening, in Vitro and in Vivo Validations. Journal of Chemical Information and Modeling 2024, 64:6174-6189. (JCR: Q1; IF: 5.6) *
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Bo L, Hu L, Wang N, Sun M, Ren X, Li Z, Yao X, Jia C: Methylene blue modified graphene film as high-performance electrode towards all-in-one flexible supercapacitors with “all-graphene” structure. Journal of Power Sources 2024, 591. (JCR: Q1; IF: 8.1) *
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Cai L, He Y, Fu X, Zhuo L, Zou Q, Yao X: AEGNN-M:A 3D Graph-Spatial Co-Representation Model for Molecular Property Prediction. IEEE Journal of Biomedical and Health Informatics 2024:1-9. (JCR: Q1; IF: 6.7)
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Cai Z, Hu Z, Yao X, Liang P, Zhang H: Single-crystal structure, Hirshfeld surface and DFT analyses of chrysomycin A, a marine microbe-derived promising agent for anticancer and antimicrobial therapy. Journal of Molecular Structure 2025, 1322. (JCR: Q2; IF: 4)
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Chen Y, Du Z, Ren X, Pan C, Zhu Y, Li Z, Meng T, Yao X: mRNA-CLA: An interpretable deep learning approach for predicting mRNA subcellular localization. Methods 2024, 227:17-26. (JCR: Q1; IF: 4.2)
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Duan H, Zhang J, Gui R, Lu Y, Pang A, Chen B, Shen L, Yu H, Li J, Xu T, et al: Discovery of a Highly Potent and Selective BRD9 PROTAC Degrader Based on E3 Binder Investigation for the Treatment of Hematological Tumors. Journal of Medicinal Chemistry 2024, 67:11326-11353. (JCR: Q1; IF: 6.8) *
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Hu L, Yang K, Wang N, Sun M, Li Z, Yao X, Jia C: Redox molecule decorated polyaniline/graphene porous composite cathode materials for enhancing the energy storage of Zn-ion capacitor. Journal of Power Sources 2024, 597. (JCR: Q1; IF: 8.1) *
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Liang TL, Pan HD, Yan PY, Mi JN, Liu XC, Bao WQ, Lian LR, Zhang CF, Chen Y, Wang JR, et al: Serum taurine affects lung cancer progression by regulating tumor immune escape mediated by the immune microenvironment. Journal of Advanced Research 2024. (JCR: Q1; IF: 11.4) *
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Liu H, Fu X, Chen H, Shang J, Zhou H, Zhe W, Yao X: Developing explainable models for lncRNA-Targeted drug discovery using graph autoencoders. Future Generation Computer Systems 2024, 160:29-39. (JCR: Q1; IF: 6.2)
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lv J, Wang N, Ren X, Gan Z, Sun M, Yang S, Pian T, Yao X, Luo J, Jia C: Deep learning-assisted research on high-performance electrolyte for zinc-ion capacitors. Journal of Power Sources 2024, 621. (JCR: Q1; IF: 8.1) *
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Su H, He L, Yu X, Wang Y, Yang L, Wang X, Yao X, Luo P, Zhang Z: Structural characterization and mechanisms of macrophage immunomodulatory activity of a novel polysaccharide with a galactose backbone from the processed Polygonati Rhizoma. Journal of Pharmaceutical Analysis 2024, 14. (JCR: Q1; IF: 6.1)
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Sun M, Yang K, Wang N, Hu L, Ren X, Li Z, Jia C, Yao X: Nitrogen-doped graphene enables stable zinc anode for long-term cycling aqueous Zn-ion batteries. Applied Surface Science 2024, 648. (JCR: Q1; IF: 6.3)
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Sun Z, Liu J, Shi L, Yang M, Wang Y, Han YP, Yao X, Liang YM: New Synthetic Approaches for the Construction of Enantioenriched Molecules Bearing Quaternary Stereocenters. Advanced Synthesis and Catalysis 2024. (JCR: Q1; IF: 4.4)
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Tan S, Liu H, Yao X: LRRK2 Inhibitors as Promising Treatment for Parkinson’s Disease. ACS Chemical Neuroscience 2024. (JCR: Q2; IF: 4.1)
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Tu G, Gong Y, Yao X, Liu Q, Xue W, Zhang R: Pathways and mechanism of MRTX1133 binding to KRAS G12D elucidated by molecular dynamics simulations and Markov state models. International Journal of Biological Macromolecules 2024, 274. (JCR: Q1; IF: 7.7)
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Wang N, Liu H, Sun M, Ren X, Hu L, Li Z, Yao X, Gong Y, Jia C: Achieving Wide-Temperature-Range Sustainable Zinc-Ion Batteries via Magnesium-Doped Cathodes and Gel Electrolytes. ACS Sustainable Chemistry and Engineering 2024, 12:3527-3537. (JCR: Q1; IF: 7.1)
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Wang N, Sun M, Ren X, Hu L, Li Z, Yao X, Jia C: Extending temperature windows of practical zinc batteries by water-locking hydrated eutectic solvents. Energy Storage Materials 2024, 68. (JCR: Q1; IF: 18.9)
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Wang Q, Zhang M, Li A, Yao X, Chen Y: Unraveling the allosteric inhibition mechanism of PARP-1 CAT and the D766/770A mutation effects via Gaussian accelerated molecular dynamics and Markov state model. Computers in Biology and Medicine 2024, 168. (JCR: Q1; IF: 7)
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Wang R, Zhou Z, Wu X, Jiang X, Zhuo L, Liu M, Li H, Fu X, Yao X: An Effective Plant Small Secretory Peptide Recognition Model Based on Feature Correction Strategy. Journal of Chemical Information and Modeling 2024, 64:2798-2806. (JCR: Q1; IF: 5.6) *
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Wang T, Du Z, Zhuo L, Fu X, Zou Q, Yao X: MultiCBlo: Enhancing predictions of compound-induced inhibition of cardiac ion channels with advanced multimodal learning. International Journal of Biological Macromolecules 2024, 276. (JCR: Q1; IF: 7.7)
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Wang T, Wang W, Jiang X, Mao J, Zhuo L, Liu M, Fu X, Yao X: ML-NPI: Predicting Interactions between Noncoding RNA and Protein Based on Meta-Learning in a Large-Scale Dynamic Graph. Journal of Chemical Information and Modeling 2024, 64:2912-2920. (JCR: Q1; IF: 5.6) *
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Wu M, Wang W, Mao X, Wu Y, Jin Y, Liu T, Lu Y, Dai H, Zeng S, Huang W, et al: Discovery of a potent CDKs/FLT3 PROTAC with enhanced differentiation and proliferation inhibition for AML. European Journal of Medicinal Chemistry 2024, 275. (JCR: Q1; IF: 6) *
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Wu M, Wu Y, Jin Y, Mao X, Zeng S, Yu H, Zhang J, Jin Y, Wu Y, Xu T, et al: Discovery of an Exceptionally Orally Bioavailable and Potent HPK1 PROTAC with Enhancement of Antitumor Efficacy of Anti-PD-L1 Therapy. Journal of Medicinal Chemistry 2024, 67:13852-13878. (JCR: Q1; IF: 6.8) *
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Wu Y, Wu M, Zheng X, Yu H, Mao X, Jin Y, Wang Y, Pang A, Zhang J, Zeng S, et al: Discovery of a potent and selective PARP1 degrader promoting cell cycle arrest via intercepting CDC25C-CDK1 axis for treating triple-negative breast cancer. Bioorganic Chemistry 2024, 142. (JCR: Q1; IF: 4.5)
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Yang S, Wang N, Ren X, Sun M, Pian T, Lv J, Gan Z, Yao X, Jia C: Quenching method introduced oxygen defect type Zn2V2O7·2H2O for long-life aqueous zinc ion batteries. Journal of Power Sources 2025, 626. (JCR: Q1; IF: 8.1) *
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Yin X, Hsieh CY, Wang X, Wu Z, Ye Q, Bao H, Deng Y, Chen H, Luo P, Liu H, et al: Enhancing Generic Reaction Yield Prediction through Reaction Condition-Based Contrastive Learning. Research 2024, 7. (JCR: Q1; IF: 8.5)
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Zhang YZ, Lai HL, Huang C, Jiang ZB, Yan HX, Wang XR, Xie C, Huang JM, Ren WK, Li JX, et al: Tanshinone IIA induces ER stress and JNK activation to inhibit tumor growth and enhance anti-PD-1 immunotherapy in non-small cell lung cancer. Phytomedicine 2024, 128. (JCR: Q1; IF: 6.7)
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Zheng JY, Luo Y, Ou TT, Zhang XJ, Lao YQ, Feng N, Peng JB, Zhang XZ, Yao X, Ma AJ: Acid-Promoted Cyclization of α-Azidobenzyl Ketones through C═N Bond Formation: Synthesis of 6-Substituted Quinoline Derivatives. Organic Letters 2024, 26:586-590. (JCR: Q1; IF: 4.9)
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Guo J, Liu H: The Applications of Molecular Dynamics Simulation in Studying Protein Structure and Dynamics. Current Medicinal Chemistry 2024, 31:2839-2840. (JCR: Q2; IF: 3.5)
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He L, Song L, Li X, Lin S, Ye G, Liu H, Zhao X: Study of andrographolide bioactivity against Pseudomonas aeruginosa based on computational methodology and biochemical analysis. Frontiers in Chemistry 2024, 12. (JCR: Q2; IF: 3.8)
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Li Q, Zhu Y, Meng X, Tong HHY, Liu H: Experiment and molecular dynamics simulations reveal proanthocyanidin B2 and B3 can inhibit prion aggregation by different mechanisms. Journal of Biomolecular Structure and Dynamics 2024, 42:2424-2436. (JCR: Q2; IF: 2.7)
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Liu S, Yu J, Ni N, Wang Z, Chen M, Li Y, Xu C, Ding Y, Zhang J, Yao X, Liu H: Versatile Framework for Drug-Target Interaction Prediction by Considering Domain-Specific Features. Journal of Chemical Information and Modeling 2024, 64:5646-5656. (JCR: Q1; IF: 5.6) *
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Ma Y, Zhu H, Jiang X, Zhou Z, Zhou Y, Tian Y, Tu L, Lu J, Niu Y, Du L, et al: Synthesis and Biological Activity of 2-Chloro-8-methoxy-5-methyl-5H-indolo [2,3-b] Quinoline for the Treatment of Colorectal Cancer by Modulating PI3K/AKT/mTOR Pathways. ACS Omega 2024, 9:30698-30707. (JCR: Q2; IF: 3.7)
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Qiu J, Yan X, Tian Y, Li Q, Liu X, Yang Y, Tong HHY, Liu H: PTB-DDI: An Accurate and Simple Framework for Drug–Drug Interaction Prediction Based on Pre-Trained Tokenizer and BiLSTM Model. International Journal of Molecular Sciences 2024, 25. (JCR: Q1; IF: 4.9)
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Qiu X, Zhang Q, Li Z, Zhang J, Liu H: Revealing the Interaction Mechanism between Mycobacterium tuberculosis GyrB and Novobiocin, SPR719 through Binding Thermodynamics and Dissociation Kinetics Analysis. International Journal of Molecular Sciences 2024, 25. (JCR: Q1; IF: 4.9)
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Tan S, Gong X, Liu H, Yao X: Identification of novel LRRK2 inhibitors by structure-based virtual screening and alchemical free energy calculation. Physical Chemistry Chemical Physics 2024, 26:19775-19786. (JCR: Q1; IF: 2.9)
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Tian Y, Wang C, Lu R, Tong HHY, Gong X, Qiu J, Peng S, Yao X, Liu H: 3DSGIMD: An accurate and interpretable molecular property prediction method using 3D spatial graph focusing network and structure-based feature fusion. Future Generation Computer Systems 2024, 161:189-200. (JCR: Q1; IF: 6.2)
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Xu P, Huang Z, Xu Y, Liu H, Liu Y, Wang L: Editorial: Antioxidants and inflammatory immune-related diseases. Frontiers in Immunology 2024, 15. (JCR: Q1; IF: 5.7)
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Yan X, Qu C, Li Q, Zhu L, Tong HHY, Liu H, Ouyang Q, Yao X: Multiscale calculations reveal new insights into the reaction mechanism between KRASG12C and α, β-unsaturated carbonyl of covalent inhibitors. Computational and Structural Biotechnology Journal 2024, 23:1408-1417. (JCR: Q2; IF: 4.4)
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Yao L, Ling B, Zhao S, Yu F, Liu H, Wang S, Xiao J: Versatile Self-Assembly of Triblock Peptides into Stable Collagen Mimetic Heterotrimers. International Journal of Molecular Sciences 2024, 25. (JCR: Q1; IF: 4.9)
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Zhong H, Liu H, Liu H: Molecular Mechanism of Tau Misfolding and Aggregation: Insights from Molecular Dynamics Simulation. Current Medicinal Chemistry 2024, 31:2855-2871. (JCR: Q2; IF: 3.5)
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Dou, Y., Li, W., Zheng, Y., Yao, X., Liu, H., Zomaya, A. Y., & Peng, S. Quick-MIMIC: A Multimodal Data Extraction Pipeline for MIMIC with Parallelization. Big Data Mining and Analytics 2024, 7(4), 1333-1346. (IF: 7.7)
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Cui Y, Wei L, Wang R, Ye X, Sakurai T: Identification of Spatial Domains, Spatially Variable Genes, and Genetic Association Studies of Alzheimer Disease with an Autoencoder-based Fuzzy Clustering Algorithm. Current Bioinformatics 2024, 19:765-776. (JCR: Q2; IF: 2.4)
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Fang Y, Luo M, Ren Z, Wei L, Wei DQ: CELA-MFP: a contrast-enhanced and label-adaptive framework for multi-functional therapeutic peptides prediction. Briefings in Bioinformatics 2024, 25. (JCR: Q1; IF: 6.8) *
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Fu X, Yang C, Su Y, Liu C, Qiu H, Yu Y, Su G, Zhang Q, Wei L, Cui F, et al: Machine Learning Enables Comprehensive Prediction of the Relative Protein Abundance of Multiple Proteins on the Protein Corona. Research 2024, 7. (JCR: Q1; IF: 8.5) *
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Jia Y, Zhang Z, Yan S, Zhang Q, Wei L, Cui F: Voting-ac4C:Pre-trained large RNA language model enhances RNA N4-acetylcytidine site prediction. International Journal of Biological Macromolecules 2024, 282. (JCR: Q1; IF: 7.7)
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Rao B, Han B, Wei L, Zhang Z, Jiang X, Manavalan B: CFCN: An HLA-peptide Prediction Model based on Taylor Extension Theory and Multi-view Learning. Current Bioinformatics 2024, 19:977-990. (JCR: Q2; IF: 2.4)
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Sangaraju VK, Pham NT, Wei L, Yu X, Manavalan B: mACPpred 2.0: Stacked Deep Learning for Anticancer Peptide Prediction with Integrated Spatial and Probabilistic Feature Representations. Journal of Molecular Biology 2024, 436. (JCR: Q1; IF: 4.7)
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Sun Y, Pan Z, Wang Z, Wang H, Wei L, Cui F, Zou Q, Zhang Z: Single-cell transcriptome analysis reveals immune microenvironment changes and insights into the transition from DCIS to IDC with associated prognostic genes. Journal of Translational Medicine 2024, 22. (JCR: Q1; IF: 6.1)
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Wang D, Jin J, Li Z, Wang Y, Fan M, Liang S, Su R, Wei L: StructuralDPPIV: a novel deep learning model based on atom structure for predicting dipeptidyl peptidase-IV inhibitory peptides. Bioinformatics 2024, 40. (JCR: Q1; IF: 4.4)
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Wei L: Advanced deep learning approaches enable high-throughput biological and biomedicine data analysis. Methods 2024, 230:116-118. (JCR: Q1; IF: 4.2)
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Wei L, Zou Q, Zeng X: Editorial: Artificial intelligence in drug discovery and development. Methods 2024, 226:133-137. (JCR: Q1; IF: 4.2)
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Yin C, Wang R, Qiao J, Shi H, Duan H, Jiang X, Teng S, Wei L: NanoCon: contrastive learning-based deep hybrid network for nanopore methylation detection. Bioinformatics 2024, 40. (JCR: Q1; IF: 4.4)
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Zhang W, Ding Y, Wei L, Guo X, Ni F: Therapeutic peptides identification via kernel risk sensitive loss-based k-nearest neighbor model and multi-Laplacian regularization. Briefings in Bioinformatics 2024, 25. (JCR: Q1; IF: 6.8) *
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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. Journal of Agricultural and Food Chemistry 2024, 72:1539-1549. (JCR: Q1; IF: 5.7)
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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. Journal of Agricultural and Food Chemistry 2024, 72:15653-15661. (JCR: Q1; IF: 5.7)
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Bao Y, Xu R, Guo J: The multiple-action allosteric inhibition of TYK2 by deucravacitinib: Insights from computational simulations. Computational Biology and Chemistry 2024, 113. (JCR: Q2; IF: 2.6)
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Deng P, Dong X, Wu Z, Hou X, Mao L, Guo J, Zhao W, Peng C, Zhang Z, Peng L: Development of Glycosylation-Modified DPPA-1 Compounds as Innovative PD-1/PD-L1 Blockers: Design, Synthesis, and Biological Evaluation. Molecules 2024, 29. (JCR: Q2; IF: 4.2)
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Faris A, Alnajjar R, Guo J, Al Mughram MH, Aouidate A, Asmari M, Elhallaoui M: Computational 3D Modeling-Based Identification of Inhibitors Targeting Cysteine Covalent Bond Catalysts for JAK3 and CYP3A4 Enzymes in the Treatment of Rheumatoid Arthritis. Molecules 2024, 29. (JCR: Q2; IF: 4.2)
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He B, Guo J, Tong HHY, To WM: Artificial Intelligence in Drug Discovery: A Bibliometric Analysis and Literature Review. Mini-Reviews in Medicinal Chemistry 2024, 24:1353-1367. (JCR: Q2; IF: 3.3)
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Hu Q, Wang Z, Meng J, Li W, Guo J, Mu Y, Wang S, Zheng L, Wei Y: OpenDock: a pytorch-based open-source framework for protein–ligand docking and modelling. Bioinformatics 2024, 40. (JCR: Q1; IF: 4.4)
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Jiao F, Cui W, Wang P, Tong HHY, 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. Journal of Biomolecular Structure and Dynamics 2024. (JCR: Q2; IF: 2.7)
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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 Management Science 2024. (JCR: Q1; IF: 3.8)
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Li L, Ran T, Zhu H, Yin M, Yu W, Zou J, Li L, Ye Y, Sun H, Wang W, et al: Molecular Mechanism of Fusarium Fungus Inhibition by Phenazine-1-carboxamide. Journal of Agricultural and Food Chemistry 2024, 72:15176-15189. (JCR: Q1; IF: 5.7)
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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 Chemical Neuroscience 2024, 15:844-853. (JCR: Q2; IF: 4.1)
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Li X, Chen Z, Tang L, Guo J, Li B: The Application of Multilinear Regression Model for Quantitative Analysis on the Basis of Excitation-Emission Matrix Spectra and the Release of a Free Graphical User Interface. Symmetry 2024, 16. (JCR: Q2; IF: 2.2)
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Liu C, Wu L, Li G, Zhang H, Xiao W, Xu D, Guo J, Li W: Improved multi-search strategy A* algorithm to solve three-dimensional pipe routing design. Expert Systems with Applications 2024, 240. (JCR: Q1; IF: 7.5)
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Luo Q, Wang S, Li HY, Zheng L, Mu Y, Guo J: Benchmarking reverse docking through AlphaFold2 human proteome. Protein Science 2024, 33. (JCR: Q1; IF: 4.5)
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Niu J, Wang F, Yang C, Ye Q, Huang J, La Y, Wang Q, Dai J, Hu T, Sang L, et al: Identification of Increased Grain Length 1 (IGL1), a novel gene encoded by a major QTL for modulating grain length in rice. Theoretical and Applied Genetics 2024, 137. (JCR: Q1; IF: 4.4)
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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. Angewandte Chemie - International Edition 2024, 63. (JCR: Q1; IF: 16.1)
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Wang Z, Wang S, Li Y, Guo J, Wei Y, Mu Y, Zheng L, Li W: A new paradigm for applying deep learning to protein-ligand interaction prediction. Briefings in Bioinformatics 2024, 25. (JCR: Q1; IF: 6.8) *
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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. Journal of Biomolecular Structure and Dynamics 2024. (JCR: Q2; IF: 2.7)
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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. (JCR: Q1; IF: 4.5)
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Yang M, Li Z, Chen J, Li Y, Xu R, Wang M, Xu Y, Chen R, Ji W, Li X, et al: Structural basis for human DPP4 receptor recognition by a pangolin MERS-like coronavirus. PLoS Pathogens 2024, 20. (JCR: Q1; IF: 5.5)
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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, 278. (JCR: Q1; IF: 7.7)
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Yuan L, Guo J: PharmaRedefine: A database server for repurposing drugs against pathogenic bacteria. Methods 2024, 227:78-85. (JCR: Q1; IF: 4.2)
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Zhang Y, Guo J, Liu Y, Qu Y, Li YQ, Mu Y, Li W: An allosteric mechanism for potent inhibition of SARS-CoV-2 main proteinase. International Journal of Biological Macromolecules 2024, 265. (JCR: Q1; IF: 7.7)
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Bian L, Ge X, Feng S, Chen G, Li K, Wang X: Determination of chloropropanol esters and glycidyl esters in instant noodles based on solid-phase microextraction with chitosan-β-cyclodextrin coated fiber. Food Chemistry 2024, 442. (JCR: Q1; IF: 8.5)
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Chen G, Yuan H, Zhang L, Zhang J, Li K, Wang X: Pancreatic lipase immobilization on cellulose filter paper for inhibitors screening and network pharmacology study of anti-obesity mechanism. Talanta 2024, 280. (JCR: Q1; IF: 5.6)
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Chen S, Gao N, Li C, Zhai F, Jiang X, Zhang P, Guan J, Li K, Xiang R, Ling G: DrugSK: A Stacked Ensemble Learning Framework for Predicting Drug Combinations of Multiple Diseases. Journal of Chemical Information and Modeling 2024, 64:5317-5327. (JCR: Q1; IF: 5.6) *
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Cui X, Jing M, Ren L, Hou X, Song Q, Li K, Wang X: Correction to: Evaluation of left ventricular systolic function in patients with iron deficiency anemia based on non-invasive left ventricular pressure–strain loops (BioMedical Engineering OnLine, (2024), 23, 1, (82), 10.1186/s12938-024-01276-2). BioMedical Engineering Online 2024, 23. (JCR: Q3; IF: 2.9)
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Cui X, Jing M, Ren L, Hou X, Song Q, Li K, Wang X: Evaluation of left ventricular systolic function in patients with iron deficiency anemia based on non-invasive left ventricular pressure–strain loops. BioMedical Engineering Online 2024, 23. (JCR: Q3; IF: 2.9)
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Ge X, Feng S, Bian L, Wang M, Li K, Wang X: Determination of parabens in breast milk using stir bar sorptive extraction coupled with UHPLC-UV. Talanta 2024, 270. (JCR: Q1; IF: 5.6)
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Hong L, Wang W, Wang S, Hu W, Sha Y, Xu X, Wang X, Li K, Wang H, Gao X, et al: Software-aided efficient identification of the components of compound formulae and their metabolites in rats by UHPLC/IM-QTOF-MS and an in-house high-definition MS2 library: Sishen formula as a case. Journal of Pharmaceutical Analysis 2024, 14. (JCR: Q1; IF: 6.1)
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Huang X, Meng W, Luo T, Zhang W, Li X, Lai Y, Guo H, Tang V, Lai X, Li K, Huang M: Comparative study and suggestions on the return to school policy of students with tuberculosis. Chinese Journal of Antituberculosis 2024, 46:998-1005.
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Huili Z, Li K, Nguyen KV: Climate change: approach to intervention using expression vector for carbonic anhydrase via glycosylphosphatidylinositol. Nucleosides, Nucleotides and Nucleic Acids 2024, 43:134-145. (JCR: Q4; IF: 1.1)
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Li J, Zhai X, Liu J, Lam CK, Meng W, Wang Y, Li S, Wang Y, Li K: Integrated causal inference modeling uncovers novel causal factors and potential therapeutic targets of Qingjin Yiqi granules for chronic fatigue syndrome. Acupuncture and Herbal Medicine 2024, 4:122-133.
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Li K, Tong HHY, Chen Y, Sun Y, Wang J: The emerging roles of next-generation metabolomics in critical care nutrition. Critical Reviews in Food Science and Nutrition 2024, 64:1213-1224. (JCR: Q1; IF: 7.3)
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Li W, Dong H, Niu K, Wang HY, Cheng W, Song H, Ying AK, Zhai X, Li K, Yu H, et al: Analyzing urinary hippuric acid as a metabolic health biomarker through a supramolecular architecture. Talanta 2024, 278. (JCR: Q1; IF: 5.6)
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Li Z, Li Y, Tang X, Xing A, Lin J, Li J, Ji J, Cai T, Zheng K, Lingampelly SS, Li K: Causal Metabolomic and Lipidomic Analysis of Circulating Plasma Metabolites in Autism: A Comprehensive Mendelian Randomization Study with Independent Cohort Validation. Metabolites 2024, 14. (JCR: Q2; IF: 3.4)
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Lingampelly SS, Naviaux JC, Heuer LS, Monk JM, Li K, Wang L, Haapanen L, Kelland CA, Van de Water J, Naviaux RK: Metabolic network analysis of pre-ASD newborns and 5-year-old children with autism spectrum disorder. Communications Biology 2024, 7. (JCR: Q1; IF: 5.2)
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Lu Y, Du N, Fang X, Shu W, Liu W, Xu X, Ye Y, Xiao L, Mao R, Li K, et al: Identification of T2W hypointense ring as a novel noninvasive indicator for glioma grade and IDH genotype. Cancer Imaging 2024, 24. (JCR: Q1; IF: 3.5)
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Meng W, Pan H, Sha Y, Zhai X, Xing A, Lingampelly SS, Sripathi SR, Wang Y, Li K: Metabolic Connectome and Its Role in the Prediction, Diagnosis, and Treatment of Complex Diseases. Metabolites 2024, 14. (JCR: Q2; IF: 3.4)
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Sha Y, Jiang M, Luo G, Meng W, Zhai X, Pan H, Li J, Yan Y, Qiao Y, Yang W, Li K: HerbMet: Enhancing metabolomics data analysis for accurate identification of Chinese herbal medicines using deep learning. Phytochemical Analysis 2024. (JCR: Q2; IF: 3)
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Sha Y, Meng W, Zhai X, Xie C, Li K: Accurate Facial Landmark Detector via Multi-scale Transformer. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2024: 278-290.
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Sha Y, Zhang Q, Zhai X, Hou M, Lu J, Meng W, Wang Y, Li K, Ma J: CerviFusionNet: A multi-modal, hybrid CNN-transformer-GRU model for enhanced cervical lesion multi-classification. iScience 2024, 27. (JCR: Q1; IF: 4.6)
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Xie C, Zhai X, Chi H, Li W, Li X, Sha Y, Li K: A Novel Fusion Pruning-Processed Lightweight CNN for Local Object Recognition on Resource-Constrained Devices. IEEE Transactions on Consumer Electronics 2024. (JCR: Q1; IF: 4.3)
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Xing A, Ng HM, Jiao H, Li K, Ye Q: The Prevalence, Epidemiological, and Molecular Characterization of Methicillin-Resistant Staphylococcus aureus (MRSA) in Macau (2017–2022). Microorganisms 2024, 12. (JCR: Q2; IF: 4.1)
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Xu W, Guo R, Chen P, Li L, Gu M, Sun H, Hu L, Wang Z, Li K: Cherry growth modeling based on Prior Distance Embedding contrastive learning: Pre-training, anomaly detection, semantic segmentation, and temporal modeling. Computers and Electronics in Agriculture 2024, 221. (JCR: Q1; IF: 7.7)
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Zhang W, Zhai X, Zhang C, Cheng S, Zhang C, Bai J, Deng X, Ji J, Li T, Wang Y, et al: Regional brain structural network topology mediates the associations between white matter damage and disease severity in first-episode, Treatment-naïve pubertal children with major depressive disorder. Psychiatry Research - Neuroimaging 2024, 344. (JCR: Q3; IF: 2.1)
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Broschat SL, Siu SWI, de la Fuente-Nunez C: Editorial: Machine learning approaches to antimicrobials: discovery and resistance. Frontiers in Bioinformatics 2024, 4. (IF: 2.8)
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Sathiyajith JN, Gopi Mohan C, Siu SWI, Bhadra P: B3P3-ν: Detecting Blood-Brain Barrier Penetrating Peptides from Sequences with Nu-SVC. In 2024 5th International Conference for Emerging Technology, INCET 2024. 2024
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Li S, Wu B, Luo YL, Han W: Simulations of Functional Motions of Super Large Biomolecules with a Mixed-Resolution Model. Journal of Chemical Theory and Computation 2024, 20:2228-2245. (JCR: Q1; IF: 5.7) *
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Ugurlu SY, McDonald D, Lei H, Jones AM, Li S, Tong HY, Butler MS, He S: Cobdock: an accurate and practical machine learning-based consensus blind docking method. Journal of Cheminformatics 2024, 16. (JCR: Q1; IF: 7.1) *
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Wu B, Li S, Han W: Selective Protonation of Catalytic Dyad for γ-Secretase-Mediated Hydrolysis Revealed by Multiscale Simulations. Journal of Physical Chemistry B 2024. (JCR: Q3; IF: 2.8)
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Shaikh M, Wang D, Ghosh S: Design of magnetic polar double-double perovskite oxides through cation ordering. Physical Review B 2024, 109. (JCR: Q2; IF: 3.2)
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Zhou F, Shaikh M, Sun W, Chen F, Chen X, Li S, Tong H, Sanyal B, Wang D: Emergence of polar skyrmions in 2D Janus CrInX3 (X=Se, Te) magnets. npj 2D Materials and Applications 2024, 8. (JCR: Q1; IF: 9.1)
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Ye Z, Ouyang D: Opportunities and Challenges of Artificial Intelligence (AI) in Drug Delivery. In Exploring Computational Pharmaceutics - Ai and Modeling in Pharma 40. 2024: 10-58
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Ye Z, Wang N, Zhou J, Ouyang D: Organic crystal structure prediction via coupled generative adversarial networks and graph convolutional networks. Innovation 2024, 5. (JCR: Q1; IF: 33.2) *
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Wu Z, Wang N, Ye Z, et al: FormulationBCS: A Machine Learning Platform Based on Diverse Molecular Representations for Biopharmaceutical Classification System (BCS) Class Prediction. Molecular Pharmaceutics2024, (JCR: Q1; IF: 4.5)
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Deng S, Wu Y, Ye Z, et al: In silico prediction of metabolic stability for ester-containing molecules: Machine learning and quantum mechanical methods. Chemometrics and Intelligent Laboratory Systems2024, (JCR Q2: ; IF: 3.7)
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Zhao L, Liu B, Tong HHY, Yao X, Liu H, Zhang Q: Inhibitor binding and disruption of coupled motions in MmpL3 protein: Unraveling the mechanism of trehalose monomycolate transport. Protein Science 2024, 33. (JCR: Q1; IF: 4.5)
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Zhang C, Zhai Y, Gong Z, Duan H, She YB, Yang YF, Su A: Transfer learning across different chemical domains: virtual screening of organic materials with deep learning models pretrained on small molecule and chemical reaction data. Journal of Cheminformatics 2024, 16. (JCR: Q1; IF: 7.1) *
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Zhai S, Tan Y, Zhu C, Zhang C, Gao Y, Mao Q, Zhang Y, Duan H, Yin Y: PepExplainer: An explainable deep learning model for selection-based macrocyclic peptide bioactivity prediction and optimization. European Journal of Medicinal Chemistry 2024, 275. (JCR: Q1; IF: 6) *
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Xu W, Wu Z, Zhang C, Zhu C, Duan H: PepCARES: A Comprehensive Advanced Refinement and Evaluation System for Peptide Design and Affinity Screening. ACS Omega 2024, 9:46429-46438. (JCR: Q2; IF: 3.7)
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Wu X, Lin H, Bai R, Duan H: Deep learning for advancing peptide drug development: Tools and methods in structure prediction and design. European Journal of Medicinal Chemistry 2024, 268. (JCR: Q1; IF: 6) *
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Su Z, Wu Y, Cao K, Du J, Cao L, Wu Z, Wu X, Wang X, Song Y, Wang X, Duan H: APEX-pHLA: A novel method for accurate prediction of the binding between exogenous short peptides and HLA class I molecules. Methods 2024, 228:38-47. (JCR: Q1; IF: 4.2)
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Ma LF, Xu L, Yuan LJ, Yang X, Wu R, Bao SM, Chen YL, Duan HL, Fang L, Zhao HJ, Zhan ZJ: Discovery of NO Donor-Aurovertin Hybrids as Dual Ferroptosis and Apoptosis Inducers for Treating Triple Negative Breast Cancer. Journal of Medicinal Chemistry 2024, 67:13089-13105. (JCR: Q1; IF: 6.8) *
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Geng G, Wang L, Xu Y, Wang T, Ma W, Duan H, Zhang J, Mao A: MGDDI: A multi-scale graph neural networks for drug–drug interaction prediction. Methods 2024, 228:22-29. (JCR: Q1; IF: 4.2)
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Cao L, Xu Z, Shang T, Zhang C, Wu X, Wu Y, Zhai S, Zhan Z, Duan H: Multi_CycGT: A Deep Learning-Based Multimodal Model for Predicting the Membrane Permeability of Cyclic Peptides. Journal of Medicinal Chemistry 2024, 67:1888-1899. (JCR: Q1; IF: 6.8) *
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Xi Y, Zheng K, Deng F, Liu Y, Sun H, Zheng Y, Tong HHY, Ji Y, Zhang Y, Chen W, et al: Themis: advancing precision oncology through comprehensive molecular subtyping and optimization. Briefings in Bioinformatics 2024, 25. (JCR: Q1; IF: 6.8) *
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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. Chemical Science 2024, 16, 371–377. (JCR Q1: ; IF: 7.6)
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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. (JCR Q2: ; IF: 4.2)
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Li Y, Hou X, Liu S, Chen Z, Wu Q, He B, Guo J, Wang L, Liu C, Mao L-F. Synthesis and Activity Study of Gefitinib Derivatives Inducing Mitochondrial Apoptosis in Hela Cells. Chemical Biology & Drug Design, 2024, 104, e70035. (JCR Q2: ; IF: 3.2)
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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. Journal of Agricultural and Food Chemistry 2024, doi: 10.1021/acs.jafc.4c07865. (JCR: Q1; IF: 5.7)
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Zhang X, Meng Z, Yang C, et al. miR-210 loss leads to widespread phenotypic and gene expression changes in human 293T cells. Frontiers in Genetics, 2024, 15: 1486252. (JCR: Q2; IF: 2.8)
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Hou X, Mao L, Zhang H, et al. Synthesis of 2H-1, 4-Benzoxazin-3 (4H)-one Derivatives Modified with 1, 2, 3-Triazole and Their Anti-inflammatory Activity in LPS-induced BV-2 Cells. Frontiers in Pharmacology, 15: 1509520. (JCR: Q1; IF: 4.4)
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Yue, Yang; Cheng, Yihua; Marquet, Celine; Xiao, Chenguang; Guo, Jingjing; Li, Shu; He, Shan. Meta-learning enables complex cluster-specific few-shot binding affinity prediction for protein-protein interactions. Journal of Chemical Information and Modeling. Accept. (JCR: Q1; IF: 5.6) *
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