Antigen-specific antibody design and optimization with diffusion-based generative models for protein structures S Luo, Y Su, X Peng, S Wang, J Peng, J Ma
Advances in Neural Information Processing Systems 35, 9754-9767, 2022
222 2022 Pocket2mol: Efficient molecular sampling based on 3d protein pockets X Peng, S Luo, J Guan, Q Xie, J Peng, J Ma
International Conference on Machine Learning, 17644-17655, 2022
207 2022 3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction J Guan, WW Qian, X Peng, Y Su, J Peng, J Ma
The Eleventh International Conference on Learning Representations (ICLR 2023), 2023
169 2023 3DLinker: An E (3) Equivariant Variational Autoencoder for Molecular Linker Design Y Huang, X Peng, J Ma, M Zhang
Thirty-ninth International Conference on Machine Learning (ICML 2022), 2022
54 2022 Boosting the Cycle Counting Power of Graph Neural Networks with I Y Huang, X Peng, J Ma, M Zhang
The Eleventh International Conference on Learning Representations (ICLR 2023), 2022
52 2022 MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generation X Peng, J Guan, Q Liu, J Ma
Fortieth International Conference on Machine Learning (ICML 2023), 2023
46 2023 Characterizing the interaction conformation between T-cell receptors and epitopes with deep learning X Peng, Y Lei, P Feng, L Jia, J Ma, D Zhao, J Zeng
Nature machine intelligence 5 (4), 395-407, 2023
31 2023 Elucidation of protein–ligand interactions by multiple trajectory analysis methods N Wu, R Zhang, X Peng, L Fang, K Chen, JS Jestilä
Physical Chemistry Chemical Physics 26 (8), 6903-6915, 2024
9 2024 Linkernet: Fragment poses and linker co-design with 3d equivariant diffusion J Guan, X Peng, PQ Jiang, Y Luo, J Peng, J Ma
Advances in Neural Information Processing Systems 36, 77503-77519, 2023
9 2023 Pocket-specific 3d molecule generation by fragment-based autoregressive diffusion models X Peng, J Guan, J Peng, J Ma
6 2023 MobilePrune: Neural Network Compression via ℓ 0 Sparse Group Lasso on the Mobile System Y Shao, K Zhao, Z Cao, Z Peng, X Peng, P Li, Y Wang, J Ma
Sensors 22 (11), 4081, 2022
4 2022 Group ligands docking to protein pockets J Guan, J Li, X Zhou, X Peng, S Wang, Y Luo, J Peng, J Ma
arXiv preprint arXiv:2501.15055, 2025
1 2025 Reprogramming Pretrained Target-Specific Diffusion Models for Dual-Target Drug Design X Zhou, J Guan, Y Zhang, X Peng, L Wang, J Ma
Advances in Neural Information Processing Systems 37, 87255-87281, 2025
2025 Rag2Mol: Structure-based drug design based on Retrieval Augmented Generation P Zhang, X Peng, R Han, T Chen, J Ma
bioRxiv, 2024.10. 20.619266, 2024
2024 Geometric Representation Condition Improves Equivariant Molecule Generation Z Li, C Zhou, X Wang, X Peng, M Zhang
arXiv preprint arXiv:2410.03655, 2024
2024 Decipher Fundamental Atomic Interactions to Unify Generative Molecular Docking and Design X Peng, R Guo, Y Xu, J Guan, Y Jia, Y Huang, M Zhang, J Peng, J Sun, ...
bioRxiv, 2024.10. 17.618827, 2024
2024 