| Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models D Jiang, Z Wu, CY Hsieh, G Chen, B Liao, Z Wang, C Shen, D Cao, J Wu, ... Journal of cheminformatics 13, 1-23, 2021 | 427 | 2021 |
| Interactiongraphnet: A novel and efficient deep graph representation learning framework for accurate protein–ligand interaction predictions D Jiang, CY Hsieh, Z Wu, Y Kang, J Wang, E Wang, B Liao, C Shen, L Xu, ... Journal of medicinal chemistry 64 (24), 18209-18232, 2021 | 131 | 2021 |
| Multi-constraint molecular generation based on conditional transformer, knowledge distillation and reinforcement learning J Wang, CY Hsieh, M Wang, X Wang, Z Wu, D Jiang, B Liao, X Zhang, ... Nature Machine Intelligence 3 (10), 914-922, 2021 | 110 | 2021 |
| Do we need different machine learning algorithms for QSAR modeling? A comprehensive assessment of 16 machine learning algorithms on 14 QSAR data sets Z Wu, M Zhu, Y Kang, ELH Leung, T Lei, C Shen, D Jiang, Z Wang, D Cao, ... Briefings in bioinformatics 22 (4), bbaa321, 2021 | 109 | 2021 |
| ADMET evaluation in drug discovery. 20. Prediction of breast cancer resistance protein inhibition through machine learning D Jiang, T Lei, Z Wang, C Shen, D Cao, T Hou Journal of Cheminformatics 12, 1-26, 2020 | 63 | 2020 |
| Mining toxicity information from large amounts of toxicity data Z Wu, D Jiang, J Wang, CY Hsieh, D Cao, T Hou Journal of Medicinal Chemistry 64 (10), 6924-6936, 2021 | 52 | 2021 |
| Hyperbolic relational graph convolution networks plus: a simple but highly efficient QSAR-modeling method Z Wu, D Jiang, CY Hsieh, G Chen, B Liao, D Cao, T Hou Briefings in Bioinformatics 22 (5), bbab112, 2021 | 45 | 2021 |
| Knowledge-based BERT: a method to extract molecular features like computational chemists Z Wu, D Jiang, J Wang, X Zhang, H Du, L Pan, CY Hsieh, D Cao, T Hou Briefings in Bioinformatics 23 (3), bbac131, 2022 | 43 | 2022 |
| Featurization strategies for protein–ligand interactions and their applications in scoring function development G Xiong, C Shen, Z Yang, D Jiang, S Liu, A Lu, X Chen, T Hou, D Cao Wiley Interdisciplinary Reviews: Computational Molecular Science 12 (2), e1567, 2022 | 35 | 2022 |
| Chemistry-intuitive explanation of graph neural networks for molecular property prediction with substructure masking Z Wu, J Wang, H Du, D Jiang, Y Kang, D Li, P Pan, Y Deng, D Cao, ... Nature Communications 14 (1), 2585, 2023 | 34 | 2023 |
| VAD-MM/GBSA: a variable atomic dielectric MM/GBSA model for improved accuracy in protein–ligand binding free energy calculations E Wang, W Fu, D Jiang, H Sun, J Wang, X Zhang, G Weng, H Liu, P Tao, ... Journal of Chemical Information and Modeling 61 (6), 2844-2856, 2021 | 32 | 2021 |
| Identification of active molecules against Mycobacterium tuberculosis through machine learning Q Ye, X Chai, D Jiang, L Yang, C Shen, X Zhang, D Li, D Cao, T Hou Briefings in Bioinformatics 22 (5), bbab068, 2021 | 29 | 2021 |
| An adaptive graph learning method for automated molecular interactions and properties predictions Y Li, CY Hsieh, R Lu, X Gong, X Wang, P Li, S Liu, Y Tian, D Jiang, J Yan, ... nature machine intelligence 4 (7), 645-651, 2022 | 25 | 2022 |
| TocoDecoy: a new approach to design unbiased datasets for training and benchmarking machine-learning scoring functions X Zhang, C Shen, B Liao, D Jiang, J Wang, Z Wu, H Du, T Wang, W Huo, ... Journal of Medicinal Chemistry 65 (11), 7918-7932, 2022 | 17 | 2022 |
| SDEGen: learning to evolve molecular conformations from thermodynamic noise for conformation generation H Zhang, S Li, J Zhang, Z Wang, J Wang, D Jiang, Z Bian, Y Zhang, ... Chemical Science 14 (6), 1557-1568, 2023 | 16 | 2023 |
| Proteome-wide profiling of the covalent-Druggable cysteines with a structure-based deep graph learning network H Du, D Jiang, J Gao, X Zhang, L Jiang, Y Zeng, Z Wu, C Shen, L Xu, ... Research, 2022 | 11 | 2022 |
| Discovery of novel non-steroidal selective glucocorticoid receptor modulators by structure-and IGN-based virtual screening, structural optimization, and biological evaluation X Hu, J Pang, C Chen, D Jiang, C Shen, X Chai, L Yang, X Zhang, L Xu, ... European Journal of Medicinal Chemistry 237, 114382, 2022 | 11 | 2022 |
| ChemistGA: a chemical synthesizable accessible molecular generation algorithm for real-world drug discovery J Wang, X Wang, H Sun, M Wang, Y Zeng, D Jiang, Z Wu, Z Liu, B Liao, ... Journal of Medicinal Chemistry 65 (18), 12482-12496, 2022 | 10 | 2022 |
| How Good Are Current Docking Programs at Nucleic Acid–Ligand Docking? A Comprehensive Evaluation D Jiang, H Zhao, H Du, Y Deng, Z Wu, J Wang, Y Zeng, H Zhang, X Wang, ... Journal of Chemical Theory and Computation 19 (16), 5633-5647, 2023 | 9 | 2023 |
| Learning on topological surface and geometric structure for 3D molecular generation O Zhang, T Wang, G Weng, D Jiang, N Wang, X Wang, H Zhao, J Wu, ... Nature Computational Science 3 (10), 849-859, 2023 | 8 | 2023 |
