用隐变量生成完整原子蛋白结构,突破长度限制。
La-Proteina: Atomistic Protein Generation via Partially Latent Flow Matching
- 用粗粒度骨架+固定维度潜变量建模序列与原子细节
- 在800残基下仍能生成有效结构,超越多数基线
- 适合需要精确原子构型的蛋白质设计任务
近期许多生成模型被用于从头设计蛋白质结构,但仅有少数能直接联合生成完整原子结构和氨基酸序列。这极具挑战性,例如侧链长度在生成过程中会变化。我们提出La-Proteina,基于一种新型部分潜变量蛋白表示:显式建模粗粒度骨架,而序列与原子细节通过每残基固定维度的潜变量捕捉,从而绕过显式侧链表示的难题。在这一部分潜空间中进行流匹配,以建模序列与全原子结构的联合分布。La-Proteina在多个生成基准上达到顶尖性能,包括全原子协同设计能力、多样性与结构有效性,经详细结构分析验证。特别地,其在原子基元支架生成任务上也优于先前模型,开启关键的原子结构条件蛋白设计。此外,它可生成长达800残基的协同设计蛋白,在大多数基线崩溃失效的尺度下仍能产出有效样本,展现其可扩展性与鲁棒性。
原文摘要 · Abstract (English)
Recently, many generative models for de novo protein structure design have emerged. Yet, only few tackle the difficult task of directly generating fully atomistic structures jointly with the underlying amino acid sequence. This is challenging, for instance, because the model must reason over side chains that change in length during generation. We introduce La-Proteina for atomistic protein design based on a novel partially latent protein representation: coarse backbone structure is modeled explicitly, while sequence and atomistic details are captured via per-residue latent variables of fixed dimensionality, thereby effectively side-stepping challenges of explicit side-chain representations. Flow matching in this partially latent space then models the joint distribution over sequences and full-atom structures. La-Proteina achieves state-of-the-art performance on multiple generation benchmarks, including all-atom co-designability, diversity, and structural validity, as confirmed through detailed structural analyses and evaluations. Notably, La-Proteina also surpasses previous models in atomistic motif scaffolding performance, unlocking critical atomistic structure-conditioned protein design tasks. Moreover, La-Proteina is able to generate co-designable proteins of up to 800 residues, a regime where most baselines collapse and fail to produce valid samples, demonstrating La-Proteina's scalability and robustness.
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