Wenbiao Zhou

Zaiyun Lin, Shiqiu Yin, Lei Shi et al.

Retrosynthesis prediction is one of the fundamental challenges in organic chemistry and related fields. The goal is to find reactants molecules that can synthesize product molecules. To solve this task, we propose a new graph-to-graph transformation model, G2GT, in which the graph encoder and graph decoder are built upon the standard transformer structure. We also show that self-training, a powerful data augmentation method that utilizes unlabeled molecule data, can significantly improve the model's performance. Inspired by the reaction type label and ensemble learning, we proposed a novel weak ensemble method to enhance diversity. We combined beam search, nucleus, and top-k sampling methods to further improve inference diversity and proposed a simple ranking algorithm to retrieve the final top-10 results. We achieved new state-of-the-art results on both the USPTO-50K dataset, with top1 accuracy of 54%, and the larger data set USPTO-full, with top1 accuracy of 50%, and competitive top-10 results.

Jiahao Chen, Letian Gao, Yanhao Zhu et al.

Recent advances in generative modeling have enabled significant progress in structure-based drug design (SBDD). Existing methods typically condition molecule generation on empty binding pockets from holo complexes, overlooking informative components such as the filler (ligands and solvent). Here, we leverage low-resolution electron density (ED) derived from the filler as a physically grounded condition for \textit{de novo} drug design. We consider two types of ED, calculated and cryo-EM/X-ray, obtainable from computational or experimental sources, supporting unified pre-training and experimental integration. Compared with rigid pocket representations, experimental ED naturally captures conformational flexibility and provides a more faithful description of the binding environment. Based on this, we introduce EDMolGPT, a decoder-only autoregressive framework that generates molecules from low-resolution ED point clouds. By grounding generation in physically meaningful density signals, EDMolGPT mitigates structural bias and produces molecules with 3D conformations. Evaluations on 101 biological targets verify the effectiveness. Our project page: https://jiahaochen1.github.io/EDMolGPT_Page/.

Wei Feng, Lvwei Wang, Zaiyun Lin et al.

Generative models for molecules based on sequential line notation (e.g. SMILES) or graph representation have attracted an increasing interest in the field of structure-based drug design, but they struggle to capture important 3D spatial interactions and often produce undesirable molecular structures. To address these challenges, we introduce Lingo3DMol, a pocket-based 3D molecule generation method that combines language models and geometric deep learning technology. A new molecular representation, fragment-based SMILES with local and global coordinates, was developed to assist the model in learning molecular topologies and atomic spatial positions. Additionally, we trained a separate noncovalent interaction predictor to provide essential binding pattern information for the generative model. Lingo3DMol can efficiently traverse drug-like chemical spaces, preventing the formation of unusual structures. The Directory of Useful Decoys-Enhanced (DUD-E) dataset was used for evaluation. Lingo3DMol outperformed state-of-the-art methods in terms of drug-likeness, synthetic accessibility, pocket binding mode, and molecule generation speed.