Xiaorui Wang

PepBAN: A Deep Learning Framework with Bilinear Attention and Adversarial Learning for Peptide-Protein Interaction Prediction

Accurate prediction of the peptide-protein interaction (PepPI) is crucial for developing peptide-based therapeutics and vaccines. However, this computational task has traditionally faced significant challenges, such as the scarcity of structure data along with the corresponding label of the binding affinity for bound complexes. To address these challenges, we introduce PepBAN, a deep learning framework for modeling PepPI predictions. PepBAN incorporates two technical advancements: (1) adopting the protein language model ESM-2 to characterize proteins and ESM-2 or a graph-based foundation model for peptides without structure data and (2) leveraging the conditional domain adversarial learning to enhance generalization across a broad range of protein targets, especially when there are limited binding data. At the core of PepBAN is a bilinear attention network (BAN) that effectively learns the pattern of pairwise local interactions, enables the identification of key residues participating in the peptide-protein interactions, and offers an intuitive approach to interpret the underlying mechanisms of PepPIs via analyzing attention weights. Our numerical experiments demonstrated that PepBAN outperformed the previous state-of-the-art models across several well-established benchmark studies. Furthermore, we evaluated PepBAN's applicability in predicting cyclic peptide-protein interactions, a task that poses significant challenges due to the presence of noncanonical amino acids. These nonstandard residues require specialized handling, which most existing sequence-based PepPI prediction models did not adequately address, and we adopt an atom-resolved molecular graph approach to process cyclic peptides. Despite this complexity, PepBAN demonstrated a clear advantage by achieving a superior prediction performance and offering a distinct edge in tackling the emerging chemical space of cyclic peptides, which has great potential for novel therapeutic development. In summary, PepBAN serves as a valuable tool for advancing peptide-based drug and therapeutic development.

SynGFN: learning across chemical space with generative flow-based molecular discovery

Protein–peptide docking with a rational and accurate diffusion generative model

A virtual platform for automated hybrid organic-enzymatic synthesis planning

The integration of organic synthesis with enzymatic catalysis offers a promising route toward efficient and sustainable construction of complex molecules. While organic synthesis enables diverse transformations, enzymatic catalysis enhances stereoselectivity under mild conditions, improving cost-effectiveness and environmental impact. However, current enzymatic synthesis planning algorithms face challenges in formulating robust hybrid organic–enzymatic strategies. Key issues include the difficulty in devising hybrid planning approaches and the reliance on template-based enzyme recommendations, which limits their adaptability across diverse scenarios. Here we show ChemEnzyRetroPlanner, an open-source hybrid synthesis planning platform that combines organic and enzymatic strategies with AI-driven decision-making. The platform features advanced computational modules, including hybrid retrosynthesis planning, reaction condition prediction, plausibility evaluation, enzymatic reaction identification, enzyme recommendation, and in silico validation of enzyme active sites. A central innovation is the RetroRollout* search algorithm, which outperforms existing tools in planning synthesis routes for organic compounds and natural products across multiple datasets. ChemEnzyRetroPlanner provides an intuitive graphical interface and programmatic APIs for scalability, while leveraging the chain-of-thought strategy and the Llama3.1 model to autonomously activate hybrid synthesis strategies for diverse scenarios. The results indicate that this fully automated, open-source system holds potential value for improving the efficiency and sustainability of molecular synthesis. The integration of organic and enzymatic synthesis enhances molecule construction efficiency. Here, the authors present ChemEnzyRetroPlanner, an AI-driven platform for automated hybrid synthesis planning, improving synthesis route efficiency and sustainability.

HiCLR: Knowledge-Induced Hierarchical Contrastive Learning with Retrosynthesis Prediction Yields a Reaction Foundation Model

Reaction representation learning is of paramount importance for adopting deep-learning-based chemistry modeling to solve real-world tasks such as synthesis planning. Most prevailing models are prestrained by self-supervised objectives that rely solely on the chemical structure information. Since structurally similar reactions could possess entirely distinct properties (e.g., reaction yields) and the synthesis-related tasks are highly heterogeneous, there are inherent limitations in constructing a foundational reaction model within the existing approaches. To tackle this limitation, we propose HiCLR, a knowledge-induced hierarchical contrastive learning framework for chemical reactions, by introducing relational inductive bias to forge chemically meaningful and generally applicable reaction fingerprints. Critically, the pretraining scheme combining both retrosynthesis prediction and contrastive loss enables HiCLR to tackle generation-based and understanding-based tasks simultaneously. Comprehensive experiments demonstrate that HiCLR successfully organizes the reaction space into hierarchical global semantic clusters, aligned well with prior knowledge. Consequently, HiCLR is the first foundation model that can be broadly applied to various synthesis-related tasks, and it achieves state-of-the-art performance in reaction classification, reaction condition recommendation, reaction yield prediction, synthesis planning, and even molecular property prediction. HiCLR demonstrates clear benefits in incorporating domain knowledge to guide the learning of neural networks, expediting AI-driven advancements in chemistry.

RSGPT: a generative transformer model for retrosynthesis planning pre-trained on ten billion datapoints

Retrosynthesis planning is a crucial task in organic synthesis, and deep-learning methods have enhanced and accelerated this process. With the advancement of the emergence of large language models, the demand for data is rapidly increasing. However, available retrosynthesis data are limited to only millions. Therefore, we pioneer the utilization of the template-based algorithm to generate chemical reaction data, resulting in the production of over 10 billion reaction datapoints. A generative pretrained transformer model is subsequently developed for template-free retrosynthesis planning by pre-training on 10 billion generated data. Inspired by the strategies of large language models, we introduce reinforcement learning to capture the relationships among products, reactants, and templates more accurately. Experiments demonstrate that our model achieves state-of-the-art performance on the benchmark, with a Top-1 accuracy of 63.4%, substantially outperforming previous models. Computer-aided synthesis-planning methods have significantly assisted synthesis planning. In this work, the authors present RSGPT, a generative model pre-trained on ten billion data points, achieving state-of-the-art performance for synthesis planning

Accurate and task-agnostic modeling of enzymatic reactions through multimodal relational learning

Enzymatic reactions play an emerging role in a broad spectrum of scientific and industrial applications. The inherent complexity of enzymes, such as their substrate specificity, conformational flexibility, and the vast diversity of reactions involved, poses substantial challenges for the advanced computational prediction of enzymatic reactions with desirable accuracy. Moreover, existing approaches are mostly tailored for a specific sub-task, such as substrate prediction or binding site annotation, which limits their applicability. In this study, we introduce ERAM, a task-agnostic multimodal learning framework capable of addressing a broad range of downstream applications with both accuracy and efficiency. ERAM aligns pre-trained molecular representations from Protein Language Model with the knowledge of enzyme catalysis by modeling enzymatic reactions as multi-relational data. In enzyme retrieval tasks, ERAM achieves an improvement of 28.31% in mean average precision compared with the state-of-the-art (SOTA) method, CREEP. In substrate prediction tasks, ERAM outperforms the SOTA method ESP, achieving average improvements of 35.53% and 22.97% in Matthews correlation coefficient across two datasets. Additionally, ERAM exhibits commendable interpretability by assigning higher attention weights to binding sites, resulting in lower false-positive rates (42.36%) and higher overlap scores (70.59%) in the unsupervised binding site prediction task compared to RXNAA Mapper. By learning embeddings of substrates, enzymes, and products within a unified knowledge graph latent space, ERAM demonstrates its potential as a versatile and effective tool for enzyme catalysis research.