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學術成果年度報告 (2022 & 2023)

人工智能藥物發現中心學術成果年度報告 (2022)

  1. Liu H, Zhou Y, Song Y, Zhang Q, Kan Y, Tang X, Xiao Q, Xiang Q, Liu H, Luo Y, Bao R. Structural and Dynamics Studies of the Spcas9 Variant Provide Insights into the Regulatory Role of the REC1 Domain. ACS Catalysis. 2022, 12: 8687-8697. (JCR: Q1; IF: 12.90)
  2. Li, K., Tong, H.H.Y., Chen, Y., Sun, Y., Wang, J. The emerging roles of next-generation metabolomics in critical care nutrition (2022) Critical Reviews in Food Science and Nutrition. (JCR: Q1; IF: 11.20)
  3. Wang Z, Pan H, Sun H, Kang Y, Liu H, Cao D, Hou T. fastDRH: a webserver to predict and analyze protein-ligand complexes based on molecular docking and MM/PB(GB)SA computation. Briefings in bioinformatics. 2022, 23:bbac201. (JCR: Q1; IF: 9.50)
  4. Zhang Q, Han J, Zhu Y, Tan SY, Liu H. Binding Thermodynamics and Dissociation Kinetics Analysis Uncover the Key Structural Motifs of Phenoxyphenol Deriva-tives as the Direct InhA Inhibitors and the Hotspot Residues of InhA. International Journal of Molecular Sciences, 2022, 23:10102. (JCR: Q1; IF: 5.60)
  5. Liu, H., Tong, H.H.Y., Zhou, Z. Feasibility of thermal methods on screening, characterization and physicochemical evaluation of pharmaceutical cocrystals (2022) Journal of Thermal Analysis and Calorimetry, 147 (23), pp. 12947-12963. (JCR: Q1; IF: 4.40)
  6. Zhao H, Yu J, Weng G, Yu J, Wang E, Gao J, Liu H, Hou T, Wang Z, Kang Y. Structural view on the role of the TRD loop in regulating DNMT3A activity: a molecular dynamics study. Phys Chem Chem Phys. 2022, 24:15791-15801. (JCR: Q2; IF: 3.30)
  7. Rui Tang, Tina Bharani, Jian Ding, Kefeng Li, Ju Wen, Suchitra D Gopinath, et al. When internships disappoint. Science (LETTER). 2022, 378(6615):22-24.
  8. Liu H, Tong H H Y, Zhou Z. Feasibility of thermal methods on screening, characterization and physicochemical evaluation of pharmaceutical cocrystals[J]. Journal of Thermal Analysis and Calorimetry, 2022, 147(23): 12947-12963.
  9. Yang Y, Wu Z, Yao X, Kang Y, Hou T, Hsieh CY, Liu H. Exploring Low-Toxicity Chemical Space with Deep Learning for Molecular Generation. J Chem Inf Model. 2022 Jul 11;62(13):3191-3199. (JCR: Q1; IF: 5.6) 
  10. Shah SJA, Zhong H, Zhang Q, Liu H. Deciphering the Effect of Lysine Acetylation on the Misfolding and Aggregation of Human Tau Fragment 171IPAKTPPAPK180 Using Molecular Dynamic Simulation and the Markov State Model. Int J Mol Sci. 2022;23(5):2399. Published 2022 Feb 22.
  11. M. Li; Y. Bao; R. Xu; H. La; J. Guo, Critical Extracellular Ca2+Dependence of the Binding between PTH1R and a G-Protein Peptide Revealed by MD Simulations. ACS Chemical Neuroscience, 2022, 13, 1666. (JCR: Q2; IF: 5.0)
  12. M. Li; M. Li; Y. Xie; J. Guo, 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. (JCR: Q2; IF: 4.6)
  13. Y. Bao; M. Li; Y. Xie; J. Guo, Investigating the Permeation Mechanism of Typical Phthalic Acid Esters (PAEs) and Membrane Response Using Molecular Dynamics Simulations. Membranes, 2022, 12, 596. (JCR: Q2; IF: 4.2)
  14. M. Li; Y. Bao; R. Xu; X. Zhang; H. La; J. Guo, Mechanism of enhanced sensitivity of mutated β-adrenergic-like octopamine receptor to amitraz in honeybee Apis mellifera: An insight from MD simulations. Pest Management Science, 2022, 78, 5423. (JCR: Q1; IF: 4.1)

 

人工智能藥物發現中心學術成果年度報告 (2023)

  1. Lu R, Wang J, Li P, Li Y, Tan S, Pan Y, Liu H, Gao P, Xie G, Yao X. Improving drug-target affinity prediction via feature fusion and knowledge distillation. Briefings in Bioinformatics. 2023;24, bbad145. (JCR: Q1; IF: 9.50)
  2. Gu S, Shen C, Yu J, Zhao H, Liu H, Liu L, Sheng R, Xu L, Wang Z, Hou T, Kang Y. Can molecular dynamics simulations improve predictions of protein-ligand binding affinity with machine learning? Briefings in Bioinformatics. 2023;24, bbad008. (JCR: Q1; IF: 9.50)
  3. Yue Y, Li S, Wang L, Liu H, Tong HHY, He S. MpbPPI: A multi-Task pre-Training-based equivariant approach for the prediction of the effect of amino acid mutations on protein-protein interactions. Briefings in Bioinformatics. 2023;24, bbad310. (JCR: Q1; IF: 9.50)
  4. Huang Y, Sun P, Chen Y, Liu H, Hao G, Song B. Bioinformatics toolbox for exploring target mutation-induced drug resistance. Briefings in Bioinformatics. 2023;24, bbad033. (JCR: Q1; IF: 9.50)
  5. Tian Y, Wang X, Yao X, Liu H, Yang Y. Predicting molecular properties based on the interpretable graph neural network with multistep focus mechanism. Briefings in Bioinformatics. 2023;24, bbac534. (JCR: Q1; IF: 9.50)
  6. 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. J Med Chem. 2023 Dec 28. doi: 10.1021/acs.jmedchem.3c00996. (JCR: Q1; IF 7.3)
  7. Tang Jiawei, Li Shaohan, Wang Duo, Zheng Qi, Zhang Jing, Lu Tao, Yu Jin, Sun Litao, Sa Baisheng, Sumpter Bobby G., Huang Jingsong, Sun Weiwei. “Enriching the 2D transition metal borides via MB XMenes (M=Fe, Co, Ir): Strong correlation and magnetism.” Nanoscale Horizons, accepted. (2023) (JCR: Q1; IF: 11.684)
  8. Guo, J; Bao, Y; Li, M; Li, S; Xi, L; Xin, P; Wu, L; Liu, H; Mu, Y. Application of computational approaches in biomembranes: From structure to function. Wiley Interdisciplinary Reviews: Computational Molecular Science 2023, 13, e1679. (JCR: Q1; IF: 11.4)
  9. Wang X, Hsieh CY, Yin X, Wang J, Li Y, Deng Y, Jiang D, Wu Z, Du H, Chen H, Li Y, Liu H, Wang Y, Luo P, Hou T, Yao X. Generic Interpretable Reaction Condition Predictions with Open Reaction Condition Datasets and Unsupervised Learning of Reaction Center. Research (Wash D C). 2023,6:0231. (JCR: Q1; IF: 11.0)
  10. Xin, P; Xu, L; Dong, W; Mao, L; Guo, J; Bi, J; Zhang, S; Pei, Y; Chen, CP. Synthetic K+ Channels Constructed by Rebuilding the Core Modules of Natural K+ Channels in an Artificial System. Angewandte Chemie-International Edition 2023, 62, e202217859. (JCR: Q1; IF: 16.6)
  11. Shi X, Wang Z, Sun X, Wang Y, Liu H, Wang F, Hao G, Yang G. Toxicological data bank bridges the gap between environmental risk assessment and green organic chemical design in One Health world. Green Chemistry. 2023;25:2170-2219. (JCR: Q1; IF: 9.8)
  12. Qu C, Yan X, Li S, Liu J, Xu Z, Chen Z, Tang D, Liu H, Song G. Visible light-mediated metal-free alkyl Suzuki-Miyaura coupling of alkyl halides and alkenylboronic acids/esters: a green method for the synthesis of allyl difluoride derivatives. Green Chemistry. 2023;25:3453-3461. (JCR: Q1; IF: 9.8)
  13. 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 J Power Sources 2024, 591, 233839. (JCR: Q1; IF 9.2)
  14. Liu, C; Wu, L; Xiao, W; Li, G; Xu, D; Guo, J; Li, W. An improved heuristic mechanism ant colony optimization algorithm for solving path planning. Knowledge-Based Systems 2023, 271, 110540. (JCR: Q1; IF: 8.8)
  15. Liu, C.; Wu, L.; Li, G.; 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 2023, 122313. (JCR: Q1; IF: 8.5)
  16. Wu, L; Chen, E; Guo, Q; Xu, D; Xiao, W; Guo, J; Zhang, M. Smooth Exploration System: A novel ease-of-use and specialized module for improving exploration of whale optimization algorithm. Knowledge-Based Systems 2023, 272, 110580. (JCR: Q1; IF: 8.8)
  17. Mei, J; Wu, L; Chen, E; Xiao, W; Zhong, L; Guo, J; Li, W. A novel structural damage detection method using a hybrid IDE–BP model. Knowledge-Based Systems 2023, 273, 110606. (JCR: Q1; IF: 8.8)
  18. Gu S, Liu H, Liu L, Hou T, Kang Y. Artificial intelligence methods in kinase target profiling: Advances and challenges. Drug Discovery Today. 2023; 28, 103796. (JCR: Q1;  IF: 7.40)
  19. 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. Comput Biol Med. 2023, 168:107682. (JCR: Q1; IF: 7.7)
  20. Jin J, Wang D, Shi G, Bao J, Wang J, Zhang H, Pan P, Li D, Yao X, Liu H, Hou T, Kang Y. FFLOM: A Flow-Based Autoregressive Model for Fragment-to-Lead Optimization. Journal of Medicinal Chemistry. 2023;66(15):10808-10823. (JCR: Q1; IF: 7.30)
  21. Wen T, Wang J, Lu R, Tan S, Li P, Yao X, Liu H, Yi Z, Li L, Liu S, Gao P, Qian H. Development, validation, and evaluation of a deep learning model to screen cyclin-dependent kinase 12 inhibitors in cancers. European Journal of Medicinal Chemistry. 2023;250, 115199. (JCR: Q1; IF: 6.70)
  22. Xi, W; Zhang, Y; Wang, R; Gong, Y; He, B; Wang, H; Guo, J; Jiao, F; Jin, J. The effect of electrode thickness and electrode/electrolyte interface on the capacitive deionization behavior of the Ti3C2Tx MXene electrodes. Journal of Alloys and Compounds 2023, 947, 169701. (JCR: Q1; IF: 6.2)
  23. 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. (JCR: Q2; IF: 6.0)
  24. Yang Y, Hsieh CY, Kang Y, Hou T, Liu H, Yao X. Deep Generation Model Guided by the Docking Score for Active Molecular Design. Journal of Chemical Information and Modeling. 2023;63:2983-2991. (JCR: Q1; IF: 5.60)
  25. Ma, Y.; Zhu, H.; Jiang, X.; Zhou, Z.; Zhou, Y.; Tian, Y.; Zhang, H.; Sun, M.; Tu, L.; Lu, J.; Niu, Y. ; Liu, H.; Liu, Y. Chen, P. Biological Evaluation of 8-Methoxy2,5-dimethyl-5H-indolo[2,3-b] Quinoline as a Potential Antitumor Agent via PI3K/AKT/mTOR Signaling. Int. J. Mol. Sci. 2023, 24, 15142. (JCR: Q1; IF: 5.6)
  26. Zhao N, Zhang Q, Yu F, Yao X, Liu H. The α-Synuclein Monomer May Have Different Misfolding Mechanisms in the Induction of α-Synuclein Fibrils with Different Polymorphs. Biomolecules. 2023;13,682. (JCR: Q1; IF: 5.50)
  27. 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. Frontiers in Pharmacology 2023, 14, 1197856. (JCR: Q1; IF: 5.6)
  28. Wang F, Ye W, He Y, Zhong H, Zhu Y, Han J, Gong X, Tian Y, Wang Y, Wang S, Ji S, Liu H, Yao X. Identification of CBPA as a New Inhibitor of PD-1/PD-L1 Interaction. International Journal of Molecular Sciences. 2023;24, 3971. (JCR: Q1; IF: 5.6)
  29. Wang Z, Zhong H, Zhang J, Pan P, Wang D, Liu H, Yao X, Hou T, Kang Y. Small-Molecule Conformer Generators: Evaluation of Traditional Methods and AI Models on High-Quality Data Sets. Journal of Chemical Information and Modeling 2023, in press. DOI: 10.1021/acs.jcim.3c01519. (JCR: Q1; IF: 5.60)
  30. Zhang, X; Yang, C; Meng, Z; Zhong, H; Hou, X; Wang, F; Lu, Y; Guo, J; Zeng, Y. miR-124 and VAMP3 Act Antagonistically in Human Neuroblastoma. Int J Mol Sci 2023, 24, 14877. (JCR: Q1; IF: 5.6)
  31. Yin X, Wang X, Li Y, Wang J, Wang Y, Deng Y, Hou T, Liu H, Luo P, Yao X. CODD-Pred: A Web Server for Efficient Target Identification and Bioactivity Prediction of Small Molecules. J Chem Inf Model. 2023 Oct 23;63(20):6169-6176. (JCR: Q1; IF: 5.6)
  32. 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. J Chem Inf Model. 2023, doi: 10.1021/acs.jcim.3c00868. (JCR: Q1; IF: 5.6)
  33. 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. (JCR: Q1; IF: 5.5)
  34. Tan S, Wang J, Gao P, Xie G, Zhang Q, Liu H, et al. Unveiling the Selectivity Mechanism of Type-I LRRK2 Inhibitors by Computational Methods: Insights from Binding Thermodynamics and Kinetics Simulation. ACS Chemical Neuroscience. 2023;14:3472-3486. (JCR: Q2; IF: 5.0)
  35. Tan S, Lu R, Yao D, Wang J, Gao P, Xie G, Liu H, Yao X. Identification of LRRK2 Inhibitors through Computational Drug Repurposing. ACS Chemical Neuroscience. 2023;14:481-493. (JCR: Q2; IF: 5.0)
  36. Ma Y, Xu H, Zhou Z, Tian Y, Du K, Zhang H, Jiang X, Lu J, Niu Y, Tu L, Liu H, Zhu H. CFNC, a neocryptolepine derivative, inhibited the growth of gastric cancer AGS cells by inhibiting PI3K/AKT signaling pathway. European Journal of Pharmacology. 2023;938, 175408. (JCR: Q1; IF: 5.0)
  37. Shah SJA, Zhang Q, Guo J, Liu H, Liu H, Villà-Freixa J. Identification of Aggregation Mechanism of Acetylated PHF6* and PHF6 Tau Peptides Based on Molecular Dynamics Simulations and Markov State Modeling. ACS Chemical Neuroscience. 2023;14:3959-3971. (JCR: Q2; IF: 5.0)
  38. 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, doi:10.1128/aac.00895-23. (JCR: Q1; IF: 4.90)
  39. Abao Xing, Henry H Y Tong, Songyan Liu, Xiaobing Zhai, Li Yu, Kefeng Li. The causal association between obesity and gastric cancer and shared molecular signatures: a large-scale Mendelian randomization and multi-omics analysis. Front Oncol. 2023, 13:1091958 (IF: 4.7, JCR Q3).
  40. 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. 2023. (JCR: Q1; IF: 4.40)
  41. Zhang Q, Han J, Zhu Y, Yu F, Hu X, Tong HHY, Liu H. Discovery of novel and potent InhA direct inhibitors by ensemble docking-based virtual screening and biological assays. Journal of Computer-Aided Molecular Design. 2023, 37, 695–706. (IF: 3.5)
  42. Chan, H.W., Chow, S., Zhang, X., Zhao, Y., Tong, H.H.Y., Chow, S.F. Inhalable Nanoparticle-based Dry Powder Formulations for Respiratory Diseases: Challenges and Strategies for Translational Research. (2023) AAPS PharmSciTech, 24 (4), art. no. 98 (JCR: Q2; IF: 3.30)
  43. Yuyang Sha, Xiaobing Zhai, Junrong Li, Weiyu Meng, Henry HY Tong, Kefeng Li. A novel lightweight deep learning fall detection system based on Global-Local attention and channel feature augmentation. Interdisciplinary Nursing Research, 2023, 2(2):68-75.
  44. Linlin Bian, Shihuan Li, Xue Ge, Mingjuan Wang, Kefeng Li, Xu Wang. Determination of bisphenols, triclosan, and parabens in bottled water by solid-phase microextraction combined with gas chromatography-tandem mass spectrometry and assessment of the associated health risk. J Food Compost Anal., 2023, 123: 105548 (IF: 4.3, JCR Q2).
  45. 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 Management Science 2023, DOI: 10.1002/ps.7699. (JCR: Q1; IF: 4.1)
  46. Li, M; Bao, Y; Li, M; Guo, J. GPCR Allostery: A View from Computational Biology. Current Medicinal Chemistry 2023, 30, 4533-4553. (JCR: Q2; IF: 4.1)
  47. Huang A, Xie X, Yao X, Liu H, Wang X, Peng S. HF-DDI: Predicting Drug-Drug Interaction Events Based on Multimodal Hybrid Fusion. Journal of Computational Biology. 2023;30:961-971. (JCR: Q2; IF: 1.70)
  48. Zhuyifan Ye, Defang Ouyang, Machine Learning Algorithms for Predicting Solubility of Small-Molecule Compounds in Organic Solvents, Pharmacy Education. (Accepted, FIP conference journal, Scopus Index)
  49. 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 Appl. Surf. Sci 2024, 648, 159008. (JCR: Q1; IF 6.7)
  50. Zhang J., Duan H., Gui R., Wu M., Shen L., Jin Y., Pang A., Yu X., Zeng S., Zhang B., Lin N., Huang W., Wang Y., Yao X., Li J., Dong X., Zhou Y., Che J. Structure-based identification of new orally bioavailable BRD9-PROTACs for treating acute myelocytic leukemia 2023 ,Eur. J Med Chem, 262, 115872 (JCR: Q1; IF 6.7)
  51. Wu Z, Wu Y, Zhu C, Wu X, Zhai S, Wang X, Su Z, Duan H. Efficient Computational Framework for Target-Specific Active Peptide Discovery: A Case Study on IL-17C Targeting Cyclic Peptides. J Chem Inf Model. 2023. Accept. (JCR: Q1; IF: 5.6)
  52. Prithwijit Mandal, Shashank Kumar Ojha, Duo Wang, Ranjan Kumar Patel, Siddharth Kumar, Jyotirmay Maity, Zhan Zhang, Hua Zhou, Christoph Klewe, Padraic Shafer, Biplab Sanyal, and Srimanta Middey. “Orthorhombic distortion drives orbital ordering in the antiferromagnetic 3d1 Mott insulator.” Physical Review B 108, 045145 (2023). (JCR: Q2; IF: 4.904)
  53. Xin Chen, Duo Wang, Linyang Li, Biplab Sanyal. “Giant spin-splitting and tunable spin-momentum locked transport in room temperature collinear antiferromagnetic semimetallic CrO monolayer.” Appl. Phys. Lett. 123, 022402 (2023) (JCR: Q1; IF: 3.971) 
  54. Yuyang Sha, Weiyu Meng, Xiaobing Zhai, Can Xie, Kefeng Li. Accurate Facial Landmark Detector via Multi-scale Transformer. PRCV 2023. (Accepted, CCF-C conference, Scoups indexed)
  55. Wei, Q., Wang, R., Jiang, Y., Wei, L., Sun, Y., Geng, J., & Su, R. (2023). ConPep: Prediction of peptide contact maps with pre-trained biological language model and multi-view feature extracting strategy. Computers in biology and medicine, 167, 107631. (JCR: Q1; IF: 7.7)
  56. Pang C, Tong H H Y, Wei L. Advanced deep learning methods for molecular property prediction[J]. Quantitative Biology, 2023. (IF: 3.1)
  57. Yaxuan Cui, Leyi Wei, Ruheng Wang, Xiucai Ye, Tetsuya Sakurai. Identification of spatial domains, spatially variable genes, and genetic association studies of Alzheimer disease with an autoencoder-based fuzzy clustering algorithm. 2023. Current Bioinformatics. (Accepted. JCR:Q1; IF: 4.0)
  58. Gong Y, Ding W, Wang P, Wu Q, Yao X*, Yang Q*. Evaluating Machine Learning Methods of Analyzing Multiclass Metabolomics. J Chem Inf Model. 2023 Dec 25;63(24):7628-7641. (JCR: Q1; IF 5.6)
  59. Zhuo L, Wang R, Fu X*, Yao X*. StableDNAm: towards a stable and efficient model for predicting DNA methylation based on adaptive feature correction learning. BMC Genomics. 2023 Dec 5;24(1):742. (JCR: Q1; IF 4.4)
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