An All-Atom Generative Model for Designing Protein Complexes

• URL: http://arxiv.org/abs/2504.13075v1
• Date: Thu, 17 Apr 2025 16:37:41 GMT
• Title: An All-Atom Generative Model for Designing Protein Complexes
• Authors: Ruizhe Chen, Dongyu Xue, Xiangxin Zhou, Zaixiang Zheng, Xiangxiang Zeng, Quanquan Gu,
• Abstract summary: APM (All-Atom Protein Generative Model) is a model specifically designed for modeling multi-chain proteins.<n>By integrating atom-level information and leveraging data on multi-chain proteins, APM is capable of precisely modeling inter-chain interactions and designing protein complexes with binding capabilities from scratch.
• Score: 49.09672038729524
• License: http://creativecommons.org/licenses/by-nc-nd/4.0/
• Abstract: Proteins typically exist in complexes, interacting with other proteins or biomolecules to perform their specific biological roles. Research on single-chain protein modeling has been extensively and deeply explored, with advancements seen in models like the series of ESM and AlphaFold. Despite these developments, the study and modeling of multi-chain proteins remain largely uncharted, though they are vital for understanding biological functions. Recognizing the importance of these interactions, we introduce APM (All-Atom Protein Generative Model), a model specifically designed for modeling multi-chain proteins. By integrating atom-level information and leveraging data on multi-chain proteins, APM is capable of precisely modeling inter-chain interactions and designing protein complexes with binding capabilities from scratch. It also performs folding and inverse-folding tasks for multi-chain proteins. Moreover, APM demonstrates versatility in downstream applications: it achieves enhanced performance through supervised fine-tuning (SFT) while also supporting zero-shot sampling in certain tasks, achieving state-of-the-art results. Code will be released at https://github.com/bytedance/apm.

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