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bioRxiv · 10.64898/2025.12.01.691647

A Unified Multi-modal LLM for Dynamic Protein-Ligand Interactions and Generative Molecular Design

Jing, H.·Miao, Y.
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Abstract

BioDynaGen (Biological Dynamics and Generation) is a novel multi-modal framework unifying protein sequences, dynamic binding site conformations, small molecule ligand SMILES, and natural language text into a single discrete token representation. Built upon a general large language model, BioDynaGen employs continuous pre-training and instruction fine-tuning via next-token prediction to address critical gaps in modeling protein dynamics and ligand interactions. This framework enables a diverse range of tasks, including small molecule-protein binding prediction, dynamic pocket design, and ligand-assisted functional generation. By comprehensively integrating these modalities, BioDynaGen offers an advanced framework for understanding and designing complex biological molecular interactions.

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Jing, H., Miao, Y.. 2025-12-03. A Unified Multi-modal LLM for Dynamic Protein-Ligand Interactions and Generative Molecular Design. https://doi.org/10.64898/2025.12.01.691647

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