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Yuchen Zhu

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#machine learning Aug 2025

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.

Shuaiyan Li, Xiaorui Wang, Yuchen Zhu et al. · 2 citations
#machine learning Open access May 2025

Token-Mol 1.0: tokenized drug design with large language models

The integration of large language models (LLMs) into drug design is gaining momentum; however, existing approaches often struggle to effectively incorporate three-dimensional molecular structures. Here, we present Token-Mol, a token-only 3D drug design model that encodes both 2D and 3D structural information, along with molecular properties, into discrete tokens. Built on a transformer decoder and trained with causal masking, Token-Mol introduces a Gaussian cross-entropy loss function tailored for regression tasks, enabling superior performance across multiple downstream applications. The model surpasses existing methods, improving molecular conformation generation by over 10% and 20% across two datasets, while outperforming token-only models by 30% in property prediction. In pocket-based molecular generation, it enhances drug-likeness and synthetic accessibility by approximately 11% and 14%, respectively. Notably, Token-Mol operates 35 times faster than expert diffusion models. In real-world validation, it improves success rates and, when combined with reinforcement learning, further optimizes affinity and drug-likeness, advancing AI-driven drug discovery. In this work the authors present Token-Mol, a token-only 3D drug design model, which deploys the Gaussian cross-entropy (GCE) loss function for regression tasks. It exhibits superior performance in molecular conformation generation, property prediction, and pocket-based generation, thus opening up new avenues for drug design.

Jike Wang, Rui Qin, Mingyang Wang et al. · 30 citations · ⚡1