尹志 (2024-05-30 15:52):
#paper  Protein Conformation Generation via Force-Guided SE(3) Diffusion Models  https://doi.org/10.48550/arXiv.2403.14088 字节跳动的一个新工作,还是蛋白质构象生成,还是SE(3) diffusion model, 不过区别于常见的静态构象的生成,这个工作提出了动态构象的生成, 这当然有意义的多,毕竟真实世界的蛋白质构象是动态的,是一个构象分布。文章引入物理信息作为guidance,这个思路很有意思,因为这样既可以 兼顾物理系统的先验,又回避了类似md这样的纯模型计算的性能问题,类似将md的计算进行了抽象,形成先验,作为guidance,然后利用生成模型进行生成。
Protein Conformation Generation via Force-Guided SE(3) Diffusion Models
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Abstract:
The conformational landscape of proteins is crucial to understanding theirfunctionality in complex biological processes. Traditional physics-basedcomputational methods, such as molecular dynamics (MD) simulations, suffer fromrare event sampling and long equilibration time problems, hindering theirapplications in general protein systems. Recently, deep generative modelingtechniques, especially diffusion models, have been employed to generate novelprotein conformations. However, existing score-based diffusion methods cannotproperly incorporate important physical prior knowledge to guide the generationprocess, causing large deviations in the sampled protein conformations from theequilibrium distribution. In this paper, to overcome these limitations, wepropose a force-guided SE(3) diffusion model, ConfDiff, for proteinconformation generation. By incorporating a force-guided network with a mixtureof data-based score models, ConfDiff can can generate protein conformationswith rich diversity while preserving high fidelity. Experiments on a variety ofprotein conformation prediction tasks, including 12 fast-folding proteins andthe Bovine Pancreatic Trypsin Inhibitor (BPTI), demonstrate that our methodsurpasses the state-of-the-art method.
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