标题： ProxelGen：生成作为三维密度的蛋白质 显示英文标题

标题： ProxelGen: Generating Proteins as 3D Densities

摘要： 我们开发了ProxelGen，这是一种蛋白质结构生成模型，它以3D密度为操作对象，而不是当前流行的3D点云表示。将蛋白质表示为体素化密度或proxels，可以实现新的任务和条件能力。我们通过结合基于3D CNN的VAE和在其潜在空间上运行的扩散模型，生成以proxels编码的蛋白质。与最先进模型相比，ProxelGen的样本在新颖性、FID分数方面表现更好，并且与训练集具有相同水平的设计性。ProxelGen的优势在标准基序支架基准中得到验证，并且我们展示了基于3D密度的生成如何允许更灵活的形状条件。 显示英文摘要

摘要： We develop ProxelGen, a protein structure generative model that operates on 3D densities as opposed to the prevailing 3D point cloud representations. Representing proteins as voxelized densities, or proxels, enables new tasks and conditioning capabilities. We generate proteins encoded as proxels via a 3D CNN-based VAE in conjunction with a diffusion model operating on its latent space. Compared to state-of-the-art models, ProxelGen's samples achieve higher novelty, better FID scores, and the same level of designability as the training set. ProxelGen's advantages are demonstrated in a standard motif scaffolding benchmark, and we show how 3D density-based generation allows for more flexible shape conditioning.