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Dejun Jiang
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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
4302021
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
1332021
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
1122021
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
1092021
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
632020
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
532021
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
462021
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
442022
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
352023
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
352022
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
322021
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
292021
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
272022
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
172022
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
162023
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
112022
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
112022
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
112022
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
102023
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
92023
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